Compositions and method for treating kidney disease

ABSTRACT

In some aspects, the disclosure relates to activin and/or GDF antagonists and methods of using activin and/or GDF antagonists to treat, prevent, or reduce the progression rate and/or severity of kidney disease, particularly treating, preventing or reducing the progression rate and/or severity of one or more kidney disease-associated complications.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a national-stage application of International Application No. PCT/US2017/055199, filed Oct. 4, 2017, which claims the benefit of U.S. Provisional Application No. 62/404,603, filed on Oct. 5, 2016. The entire contents of these applications are hereby incorporated herein by this reference in their entireties.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 19, 2017, is named APH_002_01_SL.txt and is 391,809 bytes in size.

BACKGROUND OF THE INVENTION

Kidney diseases include a range of conditions that can lead to loss of kidney function, and, in some cases, can be fatal. Normally-functioning kidneys filter wastes and excess fluids from the blood, which are then excreted in urine. When chronic kidney disease reaches an advanced stage, dangerous levels of fluid, electrolytes and wastes can build up in the bloodstream. If left untreated, kidney disease can progress to end-stage kidney failure, which is fatal without artificial filtering (dialysis) or a kidney transplant. Thus, there is a high, unmet need for effective therapies for treating kidney disease.

SUMMARY OF THE INVENTION

In part, the present disclosure relates to methods of treating kidney diseases or kidney-related disease or disorders, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist (inhibitor), or combination of activin and/or GDF antagonists (inhibitors). In certain aspects, the disclosure relates to methods of reducing the progression rate of kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of reducing the severity of kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of reducing the frequency of kidney-related disease events (e.g., kidney tissue damage, fibrosis, and/or inflammation), comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of treating one or more complications (e.g., kidney tissue damage, fibrosis, and/or inflammation) of kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of preventing one or more complication of kidney disease, comprising administering to a patient in need thereof an effective amount an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of reducing the progression rate of one or more complication of kidney disease, comprising administering to a patient in need thereof an effective amount an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In certain aspects, the disclosure relates to methods of reducing the severity of one or more complication of kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist, or combination of activin and/or GDF antagonists. In some embodiments, the method may reduce the frequency of kidney related disease events. In some embodiments, the method may reduce the severity of kidney related disease events. In some embodiments, the methods described herein relate to delaying clinical progression (worsening) of kidney disease. In some embodiments, the patient is further administered one or more supportive therapies or active agents for treating kidney disease in addition to the one or more activin and/or GDF antagonists. For example, the patient also may be administered one or more supportive therapies or active agents, e.g., angiotensin-converting enzyme (ACE) inhibitors, angiotensin II receptor blockers, a water pill or diuretics, optionally with a low-salt diet), statins, hormone erythropoietin, optionally with iron supplement, intravenous (IV) fluid supplement, calcium and/or vitamin D supplement, a phosphate binder, calcium, glucose or sodium polystyrene sulfonate (Kayexalate, Kionex), hemodialysis, peritoneal dialysis, and/or kidney transplant. Some exemplary medications for kidney diseases are Lasix® (furosemide), Demadex® (torsemide), Edecrin® (ethacrynic acid), and sodium edecrin. In certain preferred embodiments, an activin and/or GDF antagonist to be used in accordance with the methods described herein in is an inhibitor (antagonist), or combination of inhibitors (antagonists), of one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least GDF11 (e.g., a GDF11 antagonist). Effects on GDF11 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least GDF11. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least GDF11 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit GDF11 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits GDF11 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least GDF8 (e.g., a GDF8 antagonist). Effects on GDF8 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least GDF8. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least GDF8 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit GDF8 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits GDF8 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least GDF3 (e.g., a GDF3 antagonist). Effects on GDF3 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least GDF3. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least GDF3 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit GDF3 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits GDF3 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least GDF1 (e.g., a GDF1 antagonist). Effects on GDF1 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least GDF1. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least GDF1 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit BMP6 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits GDF1 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least Nodal (e.g., a Nodal antagonist). Effects on Nodal inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least Nodal. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least Nodal with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit Nodal can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits Nodal may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least Cryptic (e.g., a Cryptic antagonist). Effects on Cryptic inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least Cryptic. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least Cryptic with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit Cryptic can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits Cryptic may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least Cryptic 1B (e.g., a Cryptic 1B antagonist). Effects on Cryptic 1B inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least Cryptic 1B. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least Cryptic 1B with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit Cryptic 1B can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits Cryptic 1B may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE) (e.g., an activin antagonist). Effects on activin inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least activin. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least activin with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit activin can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits activin may further inhibit one or more of: GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3. In certain preferred embodiments, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least activin B.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least ActRII (e.g., ActRIIA and/or ActRIIB) (e.g., an ActRII antagonist). Effects on ActRII inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least ActRII. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least ActRII with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit ActRII can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits ActRII may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least ALK4 (e.g., an ALK4 antagonist). Effects on ALK4 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least ALK4. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least ALK4 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit ALK4 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits ALK4 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least ALK5 (e.g., an ALK5 antagonist). Effects on ALK5 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonists, or combination of antagonist, of the disclosure may bind to at least ALK5. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least ALK5 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit ALK5 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits ALK5 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, a activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least ALK7 (e.g., an ALK7 antagonist). Effects on ALK7 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure may bind to at least ALK7. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least ALK7 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit ALK7 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits ALK7 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK4, Cryptic, Cryptic 1B, Smad2, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least Smad2 (e.g., a Smad2 antagonist). Effects on Smad2 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonists, or combination of antagonist, of the disclosure may bind to at least Smad2. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least Smad2 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit Smad2 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits Smad2 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, and Smad3.

In certain aspects, an activin and/or GDF antagonist, or combination of antagonists, to be used in accordance with methods and uses described herein is an agent that inhibits at least Smad3 (e.g., a Smad3 antagonist). Effects on Smad3 inhibition may be determined, for example, using a cell-based assay including those described herein (e.g., a Smad signaling reporter assay). Therefore, in some embodiments, an activin and/or GDF antagonists, or combination of antagonist, of the disclosure may bind to at least Smad3. Ligand binding activity may be determined, for example, using a binding affinity assay including those described herein. In some embodiments, an activin and/or GDF antagonist, or combination of antagonists, of the disclosure binds to at least Smad3 with a K_(D) of at least 1×10⁻⁷ M (e.g., at least 1×10⁻⁸ M, at least 1×10⁻⁹ M, at least 1×10⁻¹⁰ M, at least 1×10⁻¹¹ M, or at least 1×10⁻¹² M). As described herein, various activin and/or GDF antagonists that inhibit Smad3 can be used in accordance with the methods and uses described herein including, for example, ligand traps (e.g., ActRII polypeptides, follistatin polypeptides, and FLRG polypeptides), antibodies, small molecules, nucleotide sequences, and combinations thereof. In certain embodiments, an activin and/or GDF antagonist, or combination of antagonists, that inhibits Smad3 may further inhibit one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF3, GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, and Smad2.

In certain aspects, an activin and/or GDF antagonist to be used in accordance with methods and uses described herein is an ActRII polypeptide. The term “ActRII polypeptide” collectively refers to naturally occurring ActRIIA and ActRIIB polypeptides as well as truncations and variants thereof such as those described herein. Preferably, ActRII polypeptides comprise, consist essentially of, or consist of a ligand-binding domain of an ActRII polypeptide or modified (variant) form thereof. For example, in some embodiments, an ActRIIA polypeptide comprises, consists essentially of, or consists of an ActRIIA ligand-binding domain of an ActRIIA polypeptide, for example, a portion of the ActRIIA extracellular domain. Similarly, an ActRIIB polypeptide may comprise, consist essentially of, or consist of an ActRIIB ligand-binding domain of an ActRIIB polypeptide, for example, a portion of the ActRIIB extracellular domain. Preferably, ActRII polypeptides to be used in accordance with the methods described herein are soluble polypeptides.

In certain aspects, the disclosure relates compositions comprising an ActRIIA polypeptide and uses thereof. For example, in some embodiments, an ActRIIA polypeptide of the disclosure comprises an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of amino acids 30-110 of SEQ ID NO: 9 or 10. In some embodiments, an ActRIIA polypeptides of the discloses comprises an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIA beginning at a residue corresponding to any one of amino acids 21-30 (e.g., beginning at any one of amino acids 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) of SEQ ID NO: 9 and ending at a position corresponding to any one amino acids 110-135 (e.g., ending at any one of amino acids 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, or 135) of SEQ ID NO: 9. In other embodiments, an ActRIIA polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 9. In other embodiments, an ActRIIA polypeptide may comprise of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 11. In even other embodiments, an ActRIIA polypeptide may comprise of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 12. In still other embodiments, an ActRIIA polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 177. In still even other embodiments, an ActRIIA polypeptide may comprise, consist essentially of, or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 178. In still even other embodiments, an ActRIIA polypeptide may comprise, consist essentially of, or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 179.

In other aspects, the disclosure relates compositions comprising an ActRIIB polypeptide and uses thereof. For example, in some embodiments, an ActRIIB polypeptide of the disclosure comprises an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of amino acids 29-109 of SEQ ID NO: 1. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of amino acids 29-109 of SEQ ID NO: 1, wherein the ActRIIB polypeptide comprises an acidic amino acid [naturally occurring (E or D) or artificial acidic amino acid] at position 79 with respect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of amino acids 25-131 of SEQ ID NO: 1. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of amino acids 25-131 of SEQ ID NO: 1, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence starting at a residue corresponding to any one of amino acids 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 of SEQ ID NO: 1 and ending at a residue corresponding to any one of amino acids 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134 of SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence starting at a residue corresponding to any one of amino acids 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 of SEQ ID NO: 1 and ending at a residue corresponding to any one of amino acids 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134 of SEQ ID NO: 1, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 1. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 1, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 2. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 2, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 3. In other, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 3, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 4. In other, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 4, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 5. In other, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 5, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 6. In other, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 6, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 181. In other, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 181, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 182. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 182, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 184. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 184, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 187. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 187, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 188. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 189. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 190. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 192. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 192, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 193. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 193, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 196. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 196, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 197. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 198. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 199. In still even other embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 201. In some embodiments, an ActRIIB polypeptide may comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 201, wherein the ActRIIB polypeptide comprises an acidic amino acid at position 79 with respect to SEQ ID NO: 1.

As described herein, ActRII polypeptides and variants thereof may be homomultimers, for example, homodimer, homotrimers, homotetramers, homopentamers, and higher order homomultimer complexes. In certain preferred embodiments, ActRII polypeptides and variants thereof are homodimers. In certain embodiments, ActRII polypeptide dimers described herein comprise an first ActRII polypeptide covalently, or non-covalently, associated with an second ActRII polypeptide wherein the first polypeptide comprises an ActRII domain and an amino acid sequence of a first member (or second member) of an interaction pair (e.g., a constant domain of an immunoglobulin) and the second polypeptide comprises an ActRII polypeptide and an amino acid sequence of a second member (or first member) of the interaction pair.

In certain aspects, ActRII polypeptides, including variants thereof, may be fusion proteins. For example, in some embodiments, an ActRII polypeptide may be a fusion protein comprising an ActRII polypeptide domain and one or more heterologous (non-ActRII) polypeptide domains. In some embodiments, an ActRII polypeptide may be a fusion protein that has, as one domain, an amino acid sequence derived from an ActRII polypeptide (e.g., a ligand-binding domain of an ActRII receptor or a variant thereof) and one or more heterologous domains that provide a desirable property, such as improved pharmacokinetics, easier purification, targeting to particular tissues, etc. For example, a domain of a fusion protein may enhance one or more of in vivo stability, in vivo half-life, uptake/administration, tissue localization or distribution, formation of protein complexes, multimerization of the fusion protein, and/or purification. Optionally, an ActRII polypeptide domain of a fusion protein is connected directly (fused) to one or more heterologous polypeptide domains or an intervening sequence, such as a linker, may be positioned between the amino acid sequence of the ActRII polypeptide and the amino acid sequence of the one or more heterologous domains. In certain embodiments, an ActRII fusion protein comprises a relatively unstructured linker positioned between the heterologous domain and the ActRII domain. This unstructured linker may correspond to the roughly 15 amino acid unstructured region at the C-terminal end of the extracellular domain of ActRII (the “tail”), or it may be an artificial sequence of between 3 and 15, 20, 30, 50 or more amino acids that are relatively free of secondary structure. A linker may be rich in glycine and/or proline residues and may, for example, contain repeating sequences of threonine/serine and glycines. Examples of linkers include, but are not limited to, the sequences TGGG (SEQ ID NO: 217), GGG (SEQ ID NO: 223), GGGG (SEQ ID NO: 222), TGGGG (SEQ ID NO: 219), SGGGG (SEQ ID NO: 220), GGGS (SEQ ID NO: 221224), and SGGG (SEQ ID NO: 218). In some embodiments, ActRII fusion proteins may comprise a constant domain of an immunoglobulin, including, for example, the Fc portion of an immunoglobulin. For example, an amino acid sequence that is derived from an Fc domain of an IgG (IgG1, IgG2, IgG3, or IgG4), IgA (IgA1 or IgA2), IgE, or IgM immunoglobulin. For example, an Fc portion of an immunoglobulin domain may comprise, consist essentially of, or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to any one of SEQ ID NOs: 135-149. Such immunoglobulin domains may comprise one or more amino acid modifications (e.g., deletions, additions, and/or substitutions) that confer an altered Fc activity, e.g., decrease of one or more Fc effector functions. In some embodiment, an ActRII fusion protein comprises an amino acid sequence as set forth in the formula A-B-C. For example, the B portion is an N- and C-terminally truncated ActRII polypeptide, e.g., as described herein. The A and C portions may be independently zero, one, or more than one amino acids, and both A and C portions are heterologous to B. The A and/or C portions may be attached to the B portion via a linker sequence. In certain embodiments, an ActRII fusion protein comprises a leader sequence. The leader sequence may be a native ActRII leader sequence or a heterologous leader sequence. In certain embodiments, the leader sequence is a tissue plasminogen activator (TPA) leader sequence (e.g., SEQ ID NO: 215).

An ActRII polypeptide, including variants thereof, may comprise a purification subsequence, such as an epitope tag, a FLAG tag, a polyhistidine sequence, and a GST fusion. Optionally, an ActRII polypeptide comprises one or more modified amino acid residues selected from: a glycosylated amino acid, a PEGylated amino acid, a farnesylated amino acid, an acetylated amino acid, a biotinylated amino acid, and/or an amino acid conjugated to a lipid moiety. ActRII polypeptides may comprise at least one N-linked sugar, and may include two, three or more N-linked sugars. Such polypeptides may also comprise O-linked sugars. In general, it is preferable that ActRII polypeptides be expressed in a mammalian cell line that mediates suitably natural glycosylation of the polypeptide so as to diminish the likelihood of an unfavorable immune response in a patient. ActRII polypeptides may be produced in a variety of cell lines that glycosylate the protein in a manner that is suitable for patient use, including engineered insect or yeast cells, and mammalian cells such as COS cells, CHO cells, HEK cells and NSO cells. In some embodiments, an ActRII polypeptide is glycosylated and has a glycosylation pattern obtainable from a Chinese hamster ovary cell line. In some embodiments, ActRII polypeptides of the disclosure exhibit a serum half-life of at least 4, 6, 12, 24, 36, 48, or 72 hours in a mammal (e.g., a mouse or a human). Optionally, ActRII may exhibit a serum half-life of at least 6, 8, 10, 12, 14, 20, 25, or 30 days in a mammal (e.g., a mouse or a human).

In certain aspects, the disclosure provides pharmaceutical preparations comprising one or more ActRII antagonists of the present disclosure and a pharmaceutically acceptable carrier. A pharmaceutical preparation may also comprise one or more additional active agents such as a compound that is used to treat kidney disease, particularly treating or preventing one or more complications of kidney disease (e.g., kidney tissue damage, fibrosis, and/or inflammation). In general pharmaceutical preparation will preferably be pyrogen-free (meaning pyrogen free to the extent required by regulations governing the quality of products for therapeutic use).

In certain instances, when administering an ActRII antagonist, or combination of antagonists, of the disclosure to disorders or conditions described herein, it may be desirable to monitor the effects on red blood cells during administration of the ActRII antagonist, or to determine or adjust the dosing of the ActRII antagonist, in order to reduce undesired effects on red blood cells. For example, increases in red blood cell levels, hemoglobin levels, or hematocrit levels may cause undesirable increases in blood pressure.

In certain aspects, an activin and/or GDF antagonist to be used in accordance with methods and uses of the disclosure is an antibody, or combination of antibodies. In some embodiments, the antibody binds to at least ActRII (ActRIIA and/or ActRIIB) In certain embodiments, an antibody that binds to ActRII inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to ActRII inhibits one or more GDF ligands, type I receptors, or co-receptors from binding to ActRII. In certain embodiments an antibody that binds to ActRII inhibits one or more GDF ligands from binding to ActRII selected from: activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE), GDF8, GDF11, GDF1, Nodal, GDF3, Cryptic, Cryptic 1B, ALK4, ALK5, ALK7, Smad2, and Smad3. In some embodiments, the antibody binds to at least ALK4. In certain embodiments, an antibody that binds to ALK4 inhibits ALK4 signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to ALK4 inhibits one or more GDF ligands, type II receptors, or co-receptors from binding to ALK4. In certain embodiments an antibody that binds to ALK4 inhibits one or more GDF ligands from binding to ALK4 selected from: activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE), GDF8, GDF11, GDF1, Nodal, GDF3, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, the antibody binds to at least ALK5. In certain embodiments, an antibody that binds to ALK5 inhibits ALK5 signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to ALK5 inhibits one or more GDF ligands, type II receptors, or co-receptors from binding to ALK5. In certain embodiments an antibody that binds to ALK5 inhibits one or more GDF ligands from binding to ALK5 selected from: activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE), GDF8, GDF11, GDF1, Nodal, GDF3, ALK4, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, the antibody binds to at least ALK7. In certain embodiments, an antibody that binds to ALK7 inhibits ALK7 signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to ALK7 inhibits one or more GDF ligands, type II receptors, or co-receptors from binding to ALK7. In certain embodiments an antibody that binds to ALK7 inhibits one or more GDF ligands from binding to ALK7 selected from: activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE), GDF8, GDF11, GDF1, Nodal, GDF3, ALK4, ALK5, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, the antibody binds to at least GDF11. In certain embodiments, an antibody that binds to GDF11 inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to GDF11 inhibits GDF11-ActRII binding and/or GDF11-ALK binding (e.g., GDF11-ALK4, GDF11-ALK5, and/or GDF11-ALK7 binding). In some embodiments, the antibody binds to at least GDF8. In certain embodiments, an antibody that binds to GDF8 inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to GDF8 inhibits GDF8-ActRII binding and/or GDF8-ALK binding (e.g., GDF8-ALK4, GDF8-ALK5, and/or GDF8-ALK7 binding). In some embodiments, the antibody binds to at least GDF3. In certain embodiments, an antibody that binds to GDF3 inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to GDF3 inhibits GDF3-ActRII binding and/or GDF3-ALK binding (e.g., GDF3-ALK4, GDF3-ALK5, and/or GDF3-ALK7 binding). In some embodiments, the antibody binds to activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE). In certain embodiments, an antibody that binds to activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE) inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE) inhibits activin-ActRII binding and/or activin-ALK binding (e.g., activin-ALK4, activin-ALK5, and/or activin-ALK7 binding). In some embodiments, the antibody binds to activin B. In certain embodiments, an antibody that binds to activin B inhibits ActRII signaling, optionally as measured in a cell-based assay such as those described herein. In certain embodiments, an antibody that binds to activin B inhibits activin B-ActRII binding and/or activin B-ALK binding (e.g., activin B-ALK4, activin B-ALK5, and/or activin B-ALK7 binding). In some embodiments, the antibody is a multispecific antibody, or combination of multispecific antibodies that binds to one or more of ActRIIB, ActRIIA, ALK4, ALK5, ALK7, GDF11, GDF8, activin, GDF1, Nodal, GDF3, Cryptic, Cryptic 1B, Smad2, and Smad3. In certain aspects the multispecific antibody, or a combination of multispecific antibodies, inhibits signaling in a cell-based assay of one or more of: ActRIIB, GDF11, GDF8, activin, GDF3, GDF1, Nodal, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, antibody is a chimeric antibody, a humanized antibody, or a human antibody. In some embodiments, the antibody is a single-chain antibody, an F(ab′)₂ fragment, a single-chain diabody, a tandem single-chain Fv fragment, a tandem single-chain diabody, a or a fusion protein comprising a single-chain diabody and at least a portion of an immunoglobulin heavy-chain constant region.

In certain aspects, the activin and/or GDF antagonist is a small molecule inhibitor or combination of small molecule inhibitors. In some embodiments, the small molecule inhibitor is an inhibitor of at least ActRII (e.g., ActRIIA and/or ActRIIB) In some embodiments, the small molecule inhibitor is an inhibitor of at least ALK4. In some embodiments, the small molecule inhibitor is an inhibitor of at least ALK5. In some embodiments, the small molecule inhibitor is an inhibitor of at least ALK7. In some embodiments, the small molecule inhibitor is an inhibitor of at least GDF11. In some embodiments, the small molecule inhibitor is an inhibitor of at least GDF8. In some embodiments, the small molecule inhibitor is an inhibitor of at least GDF1. In some embodiments, the small molecule inhibitor is an inhibitor of at least Nodal. In some embodiments, the small molecule inhibitor is an inhibitor of at least Cryptic. In some embodiments, the small molecule inhibitor is an inhibitor of at least Cryptic 1B. In some embodiments, the small molecule inhibitor is an inhibitor of at least Smad2. In some embodiments, the small molecule inhibitor is an inhibitor of at least Smad3. In some embodiments, the small molecule inhibitor is an inhibitor of at least GDF3. In some embodiments, the small molecule inhibitor is an inhibitor of at least activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE). In some embodiments, the small molecule inhibitor is an inhibitor of at least activin B.

In certain aspects, the activin and/or GDF antagonist is a nucleic acid inhibitor or combination of nucleic acid inhibitors. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least ActRII (e.g., ActRIIA and/or ActRIIB) In some embodiments, the nucleic acid inhibitor is an inhibitor of at least ALK4. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least ALK5. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least ALK7. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least GDF11. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least GDF8. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least GDF1. In some embodiments, the small molecule inhibitor is an inhibitor of at least Nodal. In some embodiments, the small molecule inhibitor is an inhibitor of at least Cryptic. In some embodiments, the small molecule inhibitor is an inhibitor of at least Cryptic 1B. In some embodiments, the small molecule inhibitor is an inhibitor of at least Smad2. In some embodiments, the small molecule inhibitor is an inhibitor of at least Smad3. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least GDF3. In some embodiments, the nucleic acid inhibitor is an inhibitor of at least activin (e.g., activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, and activin BE). In some embodiments, the nucleic acid inhibitor is an inhibitor of at least activin B.

In certain aspects, the activin and/or GDF antagonist is a follistatin polypeptide. In some embodiments, the follistatin polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 150. In some embodiments, the follistatin polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 151. In some embodiments, the follistatin polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 152. In some embodiments, the follistatin polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 153. In some embodiments, the follistatin polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NOs: 154-160.

In certain aspects, the activin and/or GDF antagonist is a FLRG polypeptide. In some embodiments, the FLRG polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NOs: 161-164.

In certain aspects, the activin and/or GDF antagonist is a WFIKKN1 polypeptide. In some embodiments, the WFIKKN1 polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NOs: 165-167.

In certain aspects, the activin and/or GDF antagonist is a WFIKKN2 polypeptide. In some embodiments, the WFIKKN1 polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NOs: 168-172.

In certain aspects, the activin and/or GDF antagonist is a Lefty polypeptide. In some embodiments, the WFIKKN1 polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NOs: 173-174.

In certain aspects, the activin and/or GDF antagonist is a Cerberus polypeptide. In some embodiments, the WFIKKN1 polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NO: 175.

In certain aspects, the activin and/or GDF antagonist is a Coco polypeptide. In some embodiments, the WFIKKN1 polypeptide comprises an amino acid sequence that is at least 70%, 75% 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to at least one of amino acid sequences of SEQ ID NO: 176.

In certain aspects, the disclosure relates to use of one or more activin and/or GDF antagonists, optionally in combination of one or more other supportive therapies or active agents for treating kidney disease, in the manufacture of a medicament for treating, preventing, or reducing the progression rate and/or severity of kidney disease or one or more complications of kidney disease as described herein. In certain aspects, the disclosure relates to one or more activin and/or GDF antagonists, optionally in combination of one or more other supportive therapies or active agents for treating kidney disease, for use in treating, preventing, or reducing the progression rate and/or severity of a kidney disease or one or more complications of kidney disease as described herein.

The instant disclosure provides, at least, a combination of agents, e.g., antagonists of cell signaling, for therapeutic uses. Such antagonists may include at least one of activin and/or growth and differentiation factor (GDF) antagonists, including, for example, activin, GDF8, GDF11, GDF3, GDF1, Nodal, activin receptor type IIA (ActRIIA), ActRIIB, ALK4, ALK5, ALK7, Cripto-1, Cryptic, Cryptic 1B, Smad2, and Smad3. The agents may form multimeric complexes with each other through at least one covalent or noncovalent bond. Some exemplary structures of these multimeric complexes are shown in FIGS. 5 and 6. An exemplary list of possible dimers of such agents is given below:

Possible Heterodimers:

I. Type I-Type II heterodimers: ALK4:ActRIIB; ALK4:ActRIIA; ALK4:BMPRII; ALK4:MISRII; ALK5:ActRIIB; ALK5:ActRIIA; ALK5:BMPRII; ALK5:MISRII; ALK7:ActRIIB; ALK7:ActRIIA; ALK7:BMPRII; ALK7:MISRII; ALK1:ActRIIB; ALK1:ActRIIA

II. Type 1-Type 1 heterodimers: ALK1:ALK4; ALK1:ALK5; ALK1:ALK7; ALK4:ALK5; ALK4:ALK7; ALK5:ALK7

III. Type II-Type II heterodimers: ActRIIA:ActRIIB; ActRIIA:BMPRII; ActRIIA:MISRII; ActRIIB:BMPRII; ActRIIB:MISRII

IV. Co-receptor hetero-dimers: Cryptic:Cripto; Cryptic:Cryptic 1B; Cripto:Cryptic 1B; ALK1:Cryptic; ALK1:Cryptic 1B; ALK1:Cripto; ALK4:Cryptic; ALK4:Cryptic 1B; ALK4:Cripto; ALK5:Cryptic; ALK5:Cryptic 1B; ALK5:Cripto; ALK7:Cryptic; ALK7:Cryptic 1B; ALK7:Cripto; ActRIIA:Cryptic; ActRIIA:Cryptic 1B; ActRIIA:Cripto; ActRIIB:Cryptic; ActRIIB:Cryptic 1B; ActRIIB:Cripto; BMPRII:Cryptic; BMPRII:Cryptic 1B; BMPRII:Cripto; MISRII:Cryptic; MISRII:Cryptic 1B; MISRII:Cripto

Possible Homodimers:

ALK4:ALK4; ALK5:ALK5; ALK7:ALK7; ActRIIA:ActRIIA; ActRIIB:ActRIIB; Cripto:Cripto; Cryptic 1B:Cryptic 1B; Cryptic-Cryptic

Other Antagonists as Monodimers for Dimerization:

Inhibitors (e.g., antibodies, small molecule, RNA interference, etc.) of ligands (e.g., activin A, B, C, and E; GDF8; GDF11; GDF3; GDF1; and Nodal)

Inhibitors (e.g., antibodies, small molecule, RNA interference, etc.) of type I receptors (e.g., ALK4, ALK5, and ALK7)

Inhibitors (e.g., antibodies, small molecule, RNA interference, etc.) of type II receptors (e.g., ActRIIA and ActRIIB)

Inhibitors (e.g., antibodies, small molecule, RNA interference, etc.) of co-receptors (e.g., Cripto, Cryptic, and Cryptic-1B)

Inhibitors (e.g., antibodies, small molecule, RNA interference, etc.) of Smad proteins (e.g., Smad2 and Smad3)

Natural ligand traps (naturally occurring proteins that bind to one or more activin/GDF proteins) (e.g., WFIKKN1, WFIKKN2, FST, FLRG, the Dan-related proteins Cerberus and Coco, Lefty A, Lefty B, WFIKKN1 and WFIKKN2).

Oligomers and polymers may be formed using the same strategy as shown herein and at least in FIGS. 5 and 6. For example, tetramers may be formed with two identical or different heterodimers or homodimers. Monomers may be the listed antagonists themselves, or may comprise fusion proteins comprising the listed antagonists. For example, a monomer may comprise a fusion protein of ALK4 and an Fc domain, resulting in a homodimer of ALK4-Fc:ALK4-Fc or a heterodimer of ALK4-Fc and another agent (e.g., ActBRIIA-Fc). In addition, ALK4 may be fused to itself or another agent (e.g., ALK5) as a monodimer, resulting in a homodimer of ALK4-ALK4:ALK4-ALK4 or ALK4-ALK5:ALK4-ALK5, or a heterodimer comprising ALK4-ALK4 or ALK4-ALK5. Thus, the possible dimers also include those comprising the same agents fused in different orientations. For example, ALK4-ALK5:ActRIIA-ActRIIB and ALK5-ALK4:ActRIIA:ActRIIB may form different heterodimer structures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an alignment of extracellular domains of human ActRIIA (SEQ ID NO: 11) and human ActRIIB (SEQ ID NO: 3) with the residues that are deduced herein, based on composite analysis of multiple ActRIIB and ActRIIA crystal structures, to directly contact ligand indicated with boxes.

FIG. 2 shows a multiple sequence alignment of various vertebrate ActRIIB precursor proteins without their intracellular domains (including human ActRIIB precursor protein without its intracellular domain (SEQ ID NO: 16)) and human ActRIIA precursor protein without its intracellular domain (SEQ ID NO: 15), and a consensus ActRII precursor protein without intracellular domain (SEQ ID NO: 17). FIG. 2 also discloses SEQ ID NOS 25-27 and 28-29, respectively, in order of appearance.

FIG. 3 shows a multiple sequence alignment of extracellular domains of various vertebrate ActRIIA proteins (SEQ ID NOS 18-24, respectively, in order of appearance) and human ActRIIA (SEQ ID NO: 11).

FIG. 4 shows multiple sequence alignment of Fc domains from human IgG isotypes using Clustal 2.1. Hinge regions are indicated by dotted underline. Double underline indicates examples of positions engineered in IgG1 Fc (SEQ ID NO: 135) to promote asymmetric chain pairing and the corresponding positions with respect to other isotypes IgG2 (SEQ ID NO: 136), IgG3 (SEQ ID NO: 137) and IgG4 (SEQ ID NO: 139).

FIGS. 5A-5D show schematic examples of heteromeric protein complexes comprising a type I receptor polypeptide (indicated as “I”) (e.g., a polypeptide that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ALK1, ALK4, ALK5, or ALK7 protein from humans or other species such as those described herein) and a type II receptor polypeptide (indicated as “II”) (e.g., a polypeptide that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ActRIIA, ActRIIB, MISRII, or BMPRII protein from humans or other species such as those described herein.

In the illustrated embodiments, the a type I receptor polypeptide is part of a fusion polypeptide that comprises a first member of an interaction pair (“C1”), and a type II receptor polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“C2”). Suitable interaction pairs included, for example, heavy chain and/or light chain immunoglobulin interaction pairs, truncations, and variants thereof such as those described herein (e.g., Spiess et al (2015) Molecular Immunology 67(2A): 95-106). In each fusion polypeptide, a linker may be positioned between a type I receptor polypeptide or a type II receptor polypeptide and the corresponding member of the interaction pair. The first and second members of the interaction pair may be unguided, meaning that the members of the pair may associate with each other or self-associate without substantial preference, and they may have the same or different amino acid sequences. See FIG. 5A. Alternatively, the interaction pair may be a guided (asymmetric) pair, meaning that the members of the pair associate preferentially with each other rather than self-associate. See FIG. 5B. Complexes of higher order can be envisioned. See FIGS. 5C and 5D.

FIGS. 6A-6G show schematic examples of heteromeric protein complexes comprising two type I receptor polypeptide (indicated as “I”) (e.g., a polypeptide that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ALK1, ALK4, ALK5, or ALK7 protein from humans or other species such as those described herein) and two type II receptor polypeptide (indicated as “II”) (e.g., a polypeptide that is at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ActRIIA, ActRIIB, MISRII, or BMPRII protein from humans or other species such as those described herein).

In the illustrated embodiment 6A, the first type I receptor polypeptide (from left to right) is part of a fusion polypeptide that comprises a first member of an interaction pair (“C1”) and further comprises an additional first member of an interaction pair (“A1”); and the second type I receptor polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“C2”) and further comprises an first member of an interaction pair (“A2”). The first type II receptor polypeptide (from left to right) is part of a fusion polypeptide that comprises a second member of an interaction pair (“B1”); and the second type II receptor polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“B2”). A1 and A2 may be the same or different; B1 and B2 may be the same or different, and C1 and C2 may be the same or different. In each fusion polypeptide, a linker may be positioned between the type I receptor polypeptide or type II receptor polypeptide and the corresponding member of the interaction pair as well as between interaction pairs. FIG. 6A is an example of an association of unguided interaction pairs, meaning that the members of the pair may associate with each other or self-associate without substantial preference and may have the same or different amino acid sequences.

In the illustrated embodiment 6B, the first type II receptor polypeptide (from left to right) is part of a fusion polypeptide that comprises a first member of an interaction pair (“C1”) and further comprises an additional first member of an interaction pair (“A1”); and the second type II receptor ActRIIB polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“B2”). The first type I receptor polypeptide (from left to right) is part of a fusion polypeptide that comprises a second member of an interaction pair (“B1”); and the second type I receptor polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“C2”) and further comprises a first member of an interaction pair (“A2”). In each fusion polypeptide, a linker may be positioned between the type I receptor or type II receptor polypeptide and the corresponding member of the interaction pair as well as between interaction pairs. FIG. 6B is an example of an association of guided (asymmetric) interaction pairs, meaning that the members of the pair associate preferentially with each other rather than self-associate.

Suitable interaction pairs included, for example, heavy chain and/or light chain immunoglobulin interaction pairs, truncations, and variants thereof as described herein (e.g., Spiess et al (2015) Molecular Immunology 67(2A): 95-106). Complexes of higher order can be envisioned. See FIG. 6C-6F. Using similar methods, particularly those that employ light and/or heavy chain immunoglobulins, truncations, or variants thereof, interaction pairs may be used to produce heterodimers that resemble antibody Fab and F(ab′)₂ complexes (e.g., Spiess et al (2015) Molecular Immunology 67(2A): 95-106). See FIG. 6G.

FIG. 7 shows the purification of ActRIIA-hFc expressed in CHO cells, visualized by sizing column (FIG. 7A) and Coomassie stained SDS-PAGE (FIG. 7B, left lane: molecular weight standards; right lane: ActRIIA-hFc).

FIG. 8 shows the binding of ActRIIA-hFc to activin (FIG. 8A) and GDF-11 (FIG. 8B), as measured by Biacore™ assay.

FIGS. 9A and 9B show schematic examples of a heteromeric protein complex comprising an ALK4 polypeptide (e.g., a polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ALK4 protein from humans or other species as described herein), an ActRIIB polypeptide (e.g., a polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99% or 100% identical to an extracellular domain of an ActRIIB protein from humans or other species as such as those described herein), and a ligand-binding domain of an antibody (e.g., a ligand-binding domain derived from an antibody that binds to one or more ALK4:ActRIIB-binding ligands). In the illustrated embodiments, the ALK4 polypeptide is part of a fusion polypeptide that comprises a first member of an interaction pair (“C_(1”)), and further comprises an additional first member of an interaction pair (“A_(1”)). The ActRIIB polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“B_(1”)). The variable heavy chain (V_(H)) polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“C_(2”)), and further comprises a first member of an interaction pair (“A_(2”)). The variable heavy chain (V_(L)) polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“B_(2”)). In each fusion polypeptide, a linker may be positioned between the ALK4 or ActRIIB polypeptide and the corresponding member of the interaction pair, between interaction pairs, and between the V_(H) and V_(L) polypeptides and a member of the interaction pair. A₁ and A₂ may be the same or different; B₁ and B₂ may be the same or different, and C₁ and C₂ may be the same or different. Suitable interaction pairs included, for example, constant heavy chain and/or light chain immunoglobulin interaction pairs, truncations, and variants thereof as described herein (e.g., Spiess et al (2015) Molecular Immunology 67(2A): 95-106). FIG. 9A is an example of an association of guided (asymmetric) interaction pairs, meaning that the members of the pair associate preferentially with each other rather than self-associate. FIG. 9B is an example of an association of unguided interaction pairs, meaning that the members of the pair may associate with each other or self-associate without substantial preference and may have the same or different amino acid sequences.

Such antibody-ALK4:ActRIIB complexes may be useful in situations where it is desirable to further bind/antagonize an agent that is not an ALK4:ActRIIB ligand. Alternatively, such antibody-ALK4:ActRIIB complexes may be useful in situations where it is desirable to further enhance ALK4:ActRIIB ligand binding/antagonism. For example, as demonstrated by the examples herein, activin B, activin A, GDF11, and GDF8 all bind with strong affinity to an ALK4:ActRIIB heterodimer. In addition, BMP6 binds to ALK4:ActRIIB heterodimers but with weaker affinity. In certain situations where it is desirable to antagonize BMP6 activity, in addition to one or more of the high affinity-binding ligands (e.g., activin B, activin A, GDF11, and GDF8), BMP6 may be outcompeted for binding to the ALK4:ActRIIB heterodimer. In such situations, addition of BMP6-binding domain of an antibody to the ALK4:ActRIIB heteromultimer complex would improve the capacity of such protein complexes to antagonize BMP6 in addition to one or more of activin B, activin A, GDF11, and GDF8.

FIG. 10 shows schematic examples of ALK4:ActRIIB single-trap polypeptides. ALK4:ActRIIB single-trap polypeptides may contain multiple ALK4 domains (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10 or more domains), having the same or different sequences, and multiple ActRIIB domains (e.g., 1, 2, 3, 4, 5, 6, 7, 9, 10 or more domains), having the same or different sequences. These ALK4 and ActRIIB domains may be arranged in any order and may comprise one or more linker domains positions between one or more of the ALK4 and ActRIIB domains. Such ligand traps may be used as therapeutic agents to treat or prevent diseases or conditions described herein.

FIGS. 11A-11D show schematic examples of multimeric protein complex comprising at least one ALK4:ActRIIB single-chain trap polypeptides. In the illustrated embodiments 11A and 11B, a first ALK4:ActRIIB single-chain trap polypeptide (from left to right) is part of a fusion polypeptide that comprises a first member of an interaction pair (“C_(1”)); and a second ALK4:ActRIIB single-chain trap polypeptide is part of a fusion polypeptide that comprises a second member of an interaction pair (“C_(2”)). C₁ and C₂ may be the same or different. The first and second ALK4:ActRIIB single-chain trap polypeptides may be the same or different. In each fusion polypeptide, a linker may be positioned between the ALK4:ActRIIB single-chain trap polypeptide and the corresponding member of the interaction pair. Suitable interaction pairs included, for example, heavy chain and/or light chain immunoglobulin interaction pairs, truncations, and variants thereof as described herein [e.g., Spiess et al (2015) Molecular Immunology 67(2A): 95-106]. FIG. 11A is an example of an association of unguided interaction pairs, meaning that the members of the pair may associate with each other or self-associate without substantial preference and may have the same or different amino acid sequences. FIG. 11B is an example of an association of guided (asymmetric) interaction pairs, meaning that the members of the pair associate preferentially with each other rather than self-associate. Complexes of higher order can be envisioned. In addition, such ALK4:ActRIIB single-chain trap polypeptides may be similarly be associated, covalently or non-covalently, with one or more ALK4 polypeptides and/or one or more ActRIIB polypeptides. See FIG. 11C. Also, such ALK4:ActRIIB single-chain trap polypeptides may be similarly be associated, covalently or non-covalently, with one or more ligand-binding domain of an antibody (e.g., a ligand-biding domain of an antibody that binds to one or more ALK4:ActRIIB binding ligands). See FIG. 11D.

FIG. 12 shows comparative ligand binding data for an ALK4-Fc:ActRIIB-Fc heterodimeric protein complex compared to ActRIIB-Fc homodimer and ALK4-Fc homodimer. For each protein complex, ligands are ranked by k_(off), a kinetic constant that correlates well with ligand signaling inhibition, and listed in descending order of binding affinity (ligands bound most tightly are listed at the top). At left, yellow, red, green, and blue lines indicate magnitude of the off-rate constant. Solid black lines indicate ligands whose binding to heterodimer is enhanced or unchanged compared with homodimer, whereas dashed red lines indicate substantially reduced binding compared with homodimer. As shown, the ALK4-Fc:ActRIIB-Fc heterodimer displays enhanced binding to activin B compared with either homodimer, retains strong binding to activin A, GDF8, and GDF11 as observed with ActRIIB-Fc homodimer, and exhibits substantially reduced binding to BMP9, BMP10, and GDF3. Like ActRIIB-Fc homodimer, the heterodimer retains intermediate-level binding to BMP6.

FIG. 13 shows comparative ALK4-Fc:ActRIIB-Fc heterodimer/ActRIIB-Fc:ActRIIB-Fc homodimer IC₅₀ data as determined by an A-204 Reporter Gene Assay as described herein. ALK4-Fc:ActRIIB-Fc heterodimer inhibits activin A, activin B, GDF8, and GDF11 signaling pathways similarly to the ActRIIB-Fc:ActRIIB-Fc homodimer. However, ALK4-Fc:ActRIIB-Fc heterodimer inhibition of BMP9 and BMP10 signaling pathways is significantly reduced compared to the ActRIIB-Fc:ActRIIB-Fc homodimer. These data demonstrate that ALK4:ActRIIB heterodimers are more selective antagonists of activin A, activin B, GDF8, and GDF11 compared to corresponding ActRIIB:ActRIIB homodimers.

FIGS. 14A-14C show gene expression profiles of fibrotic genes (Col1a1, Fibronectin, PAI-1, CTGF, and a-SMA), inflammatory genes (TNF-alpha, and MCP1), cytokine genes (TGF-beta 1, TGF-beta 2, TGF-beta 3, and activin A), kidney injury gene (NGAL), Hypoxia-inducible factor 1-alpha (HIF1a), and activin A receptor (Acvr2A) from mouse kidneys subjected to unilateral ureteral obstruction (UUO). Samples from the contralateral, non-surgery kidney were used as a control (Ctrl). Gene expression profiles were obtained at 17 days post-surgery. Mice were administered either PBS or an ALK4-Fc:ActRIIB-Fc homodimer at days 3, 7, 10, and 14 post-surgery. ($) denotes a statistical difference between UUO kidneys at 17 days in mice administered only PBS compared UUO kidneys at 17 days in mice administered the ALK7-Fc:ActRIIB-Fc homodimer. (@) denotes that no transcript was detected.

FIG. 15 shows comparative ligand binding data for an ALK7-Fc:ActRIIB-Fc heterodimeric protein complex compared to ActRIIB-Fc homodimer and ALK7-Fc homodimer. For each protein complex, ligands are ranked by k_(off), a kinetic constant that correlates well with ligand signaling inhibition, and listed in descending order of binding affinity (ligands bound most tightly are listed at the top). At left, yellow, red, green, and blue lines indicate magnitude of the off-rate constant. Solid black lines indicate ligands whose binding to heterodimer is enhanced or unchanged compared with homodimer, whereas dashed red lines indicate substantially reduced binding compared with homodimer. As shown, four of the five ligands with strong binding to ActRIIB-Fc homodimer (activin A, BMP10, GDF8, and GDF11) exhibit reduced binding to the ActRIIB-Fc:ALK7-Fc heterodimer, the exception being activin B which retains tight binding to the heterodimer. Similarly, three of four ligands with intermediate binding to ActRIIB-Fc homodimer (GDF3, BMP6, and particularly BMP9) exhibit reduced binding to the ActRIIB-Fc:ALK7-Fc heterodimer, whereas binding to activin AC is increased to become the second strongest ligand interaction with the heterodimer overall. Finally, activin C and BMP5 unexpectedly bind the ActRIIB-Fc:ALK7 heterodimer with intermediate strength despite no binding (activin C) or weak binding (BMP5) to ActRIIB-Fc homodimer. No ligands tested bind to ALK7-Fc homodimer.

FIGS. 16A-16C show gene expression profiles of fibrotic genes (Col1a1, Col3a1, Fibronectin, PAI-1, CTGF, and a-SMA), inflammatory genes (TNF-alpha, and MCP1), cytokine genes (Tgfb1, Tgfb2, Tgfb3, and activin A), kidney injury gene (NGAL), Hypoxia-inducible factor 1-alpha (HIF1a), and activin A receptor (Acvr2A) from mouse kidneys subjected to unilateral ureteral obstruction (UUO). Samples from the contralateral, non-surgery kidney were used as a control (Ctrl). Gene expression profiles were obtained at 3 days and 17 days post-surgery. Mice were administered either PBS or an ALK7-Fc:ActRIIB-Fc homodimer at days 3, 7, 10, and 14 post-surgery. Statistical analysis was performed using a one-way ANOVA followed by Tukey analysis. (*) denotes a statistical difference between i) control samples compared to UUO kidneys at 3 days or ii) control samples compared to UUO kidneys at 17 days in mice administered the ALK7-Fc:ActRIIB-Fc homodimer. ($) denotes a statistical difference between UUO kidneys at 17 days in mice administered only PBS compared with UUO kidneys at 17 days in mice administered the ALK7-Fc:ActRIIB-Fc homodimer. (@) denotes that no transcript was detected.

FIG. 17 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIa-Fc homodimer.

FIG. 18 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIa-Fc homodimer.

FIG. 19 shows gene expression profiles of cytokine genes (Tgfb1 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIa-Fc homodimer.

FIG. 20 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIB(20-134)-Fc homodimer.

FIG. 21 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIB(20-134)-Fc homodimer.

FIG. 22 shows gene expression profiles of cytokine genes (Tgfb1 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of ActRIIB(20-134)-Fc homodimer.

FIG. 23 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-TGF-beta 1/2/3 pan antibody (i.e., binds to isoforms 1, 2, and 3 of TGF-beta).

FIG. 24 shows gene expression profiles of inflammatory gene (TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-TGF-beta 1/2/3 pan antibody (i.e., binds to isoforms 1, 2, and 3 of TGF-beta).

FIG. 25 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-TGF-beta 1/2/3 pan antibody (i.e., binds to isoforms 1, 2, and 3 of TGF-beta).

FIG. 26 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-activin A antibody.

FIG. 27 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin A antibody.

FIG. 28 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin A antibody.

FIG. 29 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-activin A/B antibody.

FIG. 30 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin A/B antibody.

FIG. 31 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin A/B antibody.

FIG. 32 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-activin B antibody.

FIG. 33 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin B antibody.

FIG. 34 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-activin B antibody.

FIG. 35 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-ActRIIA antibody.

FIG. 36 shows gene expression profiles of inflammatory gene (TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIA antibody.

FIG. 37 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIA antibody.

FIG. 38 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-ActRIIA/IIB antibody.

FIG. 39 shows gene expression profiles of inflammatory gene (TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIA/IIB antibody.

FIG. 40 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIA/IIB antibody.

FIG. 41 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an anti-ActRIIB antibody.

FIG. 42 shows gene expression profiles of inflammatory gene (TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIB antibody.

FIG. 43 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the anti-ActRIIB antibody.

FIG. 44 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an ActRIIB(L79D, 25-131)-hFc homodimer.

FIG. 45 shows gene expression profiles of inflammatory genes (IL-1B and TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the ActRIIB(L79D, 25-131)-hFc homodimer.

FIG. 46 shows gene expression profiles of cytokine genes (Tgfb1 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of the ActRIIB(L79D, 25-131)-hFc homodimer.

FIG. 49 shows ligand binding data for an ActRIIA-Fc:ALK4-Fc heterodimeric protein complex as compared to ActRIIA-Fc homodimer and ALK4-Fc homodimer. As shown, the ActRIIA-Fc:ALK4-Fc heterodimer exhibits enhanced binding to activin A, and particularly enhanced binding to activin AC, compared to ActRIIA-Fc homodimer, while retaining strong binding to activin AB and GDF11. In addition, the ligand with highest affinity for ActRIIA-Fc homodimer, activin B, displays reduced affinity (albeit still within the high-affinity range) for the ActRIIA-Fc:ALK4-Fc heterodimer. The ActRIIA-Fc:ALK4-Fc heterodimer also exhibits markedly reduced binding to BMP10 compared to ActRIIA-Fc homodimer.

FIG. 50 shows gene expression profiles of fibrotic genes (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an ALK4-Fc:ActRIIA-Fc heterodimer.

FIG. 51 shows gene expression profiles of inflammatory gene (TNF-alpha) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an ALK4-Fc:ActRIIA-Fc heterodimer.

FIG. 52 shows gene expression profiles of cytokine genes (Tgfb1/2/3 and activin A) and kidney injury gene (NGAL) from mouse kidneys subjected to unilateral ureteral obstruction (UUO) after treatment of an ALK4-Fc:ActRIIA-Fc heterodimer.

FIG. 53 shows ligand binding data for a BMPRII-Fc:ALK4-Fc heterodimeric protein complex as compared to BMPRII-Fc homodimer and ALK4-Fc homodimer. BMPRII-Fc:ALK4-Fc heterodimer differs from both homodimers by binding several activin ligands with high or intermediate strength and differs from BMPRII-Fc homodimer by binding BMP15 only weakly. Most notably, BMPRII-Fc:ALK4-Fc heterodimer binds strongly and with high selectivity to the heterodimeric ligand activin AB.

DETAILED DESCRIPTION OF THE INVENTION 1. Overview

The TGF-β superfamily includes over 30 secreted factors including TGF-betas, activins, nodals, bone morphogenetic proteins (BMPs), growth and differentiation factors (GDFs), and anti-Mullerian hormone (AMH) (Weiss et al. (2013) Developmental Biology, 2(1): 47-63). Members of the superfamily, which are found in both vertebrates and invertebrates, are ubiquitously expressed in diverse tissues and function during the earliest stages of development throughout the lifetime of an animal. Indeed, TGF-β superfamily proteins are key mediators of stem cell self-renewal, gastrulation, differentiation, organ morphogenesis, and adult tissue homeostasis. Consistent with this ubiquitous activity, aberrant TGF-beta superfamily signaling is associated with a wide range of human pathologies.

Ligands of the TGF-beta superfamily share the same dimeric structure in which the central 3-½ turn helix of one monomer packs against the concave surface formed by the beta-strands of the other monomer. The majority of TGF-beta family members are further stabilized by an intermolecular disulfide bond. This disulfide bonds traverses through a ring formed by two other disulfide bonds generating what has been termed a ‘cysteine knot’ motif (Lin et al. (2006) Reproduction 132: 179-190; and Hinck et al. (2012) FEBS Letters 586: 1860-1870).

TGF-beta superfamily signaling is mediated by heteromeric complexes of type I and type II serine/threonine kinase receptors, which phosphorylate and activate downstream SMAD proteins (e.g., SMAD proteins 1, 2, 3, 5, and 8) upon ligand stimulation [Massagué (2000) Nat. Rev. Mol. Cell Biol. 1:169-178]. These type I and type II receptors are transmembrane proteins, composed of a ligand-binding extracellular domain with cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase specificity. In general, type I receptors mediate intracellular signaling while the type II receptors are required for binding TGF-beta superfamily ligands. Type I and II receptors form a stable complex after ligand binding, resulting in phosphorylation of type I receptors by type II receptors.

The TGF-beta family can be divided into two phylogenetic branches based on the type I receptors they bind and the Smad proteins they activate. One is the more recently evolved branch, which includes, e.g., the TGF-betas, activins, GDF8, GDF9, GDF11, BMP3 and nodal, which signal through type I receptors that activate Smads 2 and 3 (Hinck (2012) FEBS Letters 586:1860-1870). The other branch comprises the more distantly related proteins of the superfamily and includes, e.g., BMP2, BMP4, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF1, GDF5, GDF6, and GDF7, which signal through Smads 1, 5, and 8.

Activins are members of the TGF-beta superfamily and were initially discovered as regulators of secretion of follicle-stimulating hormone, but subsequently various reproductive and non-reproductive roles have been characterized. There are three principal activin forms (A, B, and AB) that are homo/heterodimers of two closely related β subunits (β_(A)β_(A), β_(B)β_(B), and β_(A)β_(B), respectively). The human genome also encodes an activin C and an activin E, which are primarily expressed in the liver, and heterodimeric forms containing β_(C) or β_(E) are also known. In the TGF-beta superfamily, activins are unique and multifunctional factors that can stimulate hormone production in ovarian and placental cells, support neuronal cell survival, influence cell-cycle progress positively or negatively depending on cell type, and induce mesodermal differentiation at least in amphibian embryos (DePaolo et al. (1991) Proc Soc Ep Biol Med. 198:500-512; Dyson et al. (1997) Curr Biol. 7:81-84; and Woodruff (1998) Biochem Pharmacol. 55:953-963). In several tissues, activin signaling is antagonized by its related heterodimer, inhibin. For example, in the regulation of follicle-stimulating hormone (FSH) secretion from the pituitary, activin promotes FSH synthesis and secretion, while inhibin reduces FSH synthesis and secretion. Other proteins that may regulate activin bioactivity and/or bind to activin include follistatin (FS), follistatin-related protein (FSRP, also known as FLRG or FSTL3), and α₂-macroglobulin.

As described herein, agents that bind to “activin A” are agents that specifically bind to the β_(A) subunit, whether in the context of an isolated β_(A) subunit or as a dimeric complex (e.g., a β_(A)β_(A) homodimer or a β_(A)β_(B) heterodimer). In the case of a heterodimer complex (e.g., a β_(A)β_(B) heterodimer), agents that bind to “activin A” are specific for epitopes present within the β_(A) subunit, but do not bind to epitopes present within the non-β_(A) subunit of the complex (e.g., the β_(B) subunit of the complex). Similarly, agents disclosed herein that antagonize (inhibit) “activin A” are agents that inhibit one or more activities as mediated by a β_(A) subunit, whether in the context of an isolated β_(A) subunit or as a dimeric complex (e.g., a β_(A)β_(A) homodimer or a β_(A)β_(B) heterodimer). In the case of β_(A)β_(B) heterodimers, agents that inhibit “activin A” are agents that specifically inhibit one or more activities of the β_(A) subunit, but do not inhibit the activity of the non-β_(A) subunit of the complex (e.g., the β_(B) subunit of the complex). This principle applies also to agents that bind to and/or inhibit “activin B”, “activin C”, and “activin E”. Agents disclosed herein that antagonize “activin AB” are agents that inhibit one or more activities as mediated by the β_(A) subunit and one or more activities as mediated by the β_(B) subunit.

The BMPs and GDFs together form a family of cysteine-knot cytokines sharing the characteristic fold of the TGF-beta superfamily (Rider et al. (2010) Biochem J., 429(1):1-12). This family includes, for example, BMP2, BMP4, BMP6, BMP7, BMP2a, BMP3, BMP3b (also known as GDF10), BMP4, BMP5, BMP6, BMP7, BMP8, BMP8a, BMP8b, BMP9 (also known as GDF2), BMP10, BMP11 (also known as GDF11), BMP12 (also known as GDF7), BMP13 (also known as GDF6), BMP14 (also known as GDF5), BMP15, GDF1, GDF3 (also known as VGR2), GDF8 (also known as myostatin), GDF9, GDF15, and decapentaplegic. Besides the ability to induce bone formation, which gave the BMPs their name, the BMP/GDFs display morphogenetic activities in the development of a wide range of tissues. BMP/GDF homo- and hetero-dimers interact with combinations of type I and type II receptor dimers to produce multiple possible signaling complexes, leading to the activation of one of two competing sets of SMAD transcription factors. BMP/GDFs have highly specific and localized functions. These are regulated in a number of ways, including the developmental restriction of BMP/GDF expression and through the secretion of several specific BMP antagonist proteins that bind with high affinity to the cytokines. Curiously, a number of these antagonists resemble TGF-beta superfamily ligands.

Growth and differentiation factor-8 (GDF8) is also known as myostatin. GDF8 is a negative regulator of skeletal muscle mass and is highly expressed in developing and adult skeletal muscle. The GDF8 null mutation in transgenic mice is characterized by a marked hypertrophy and hyperplasia of skeletal muscle [McPherron et al. Nature (1997) 387:83-90]. Similar increases in skeletal muscle mass are evident in naturally occurring mutations of GDF8 in cattle and, strikingly, in humans (Ashmore et al. (1974) Growth, 38:501-507; Swatland and Kieffer, J. Anim. Sci. (1994) 38:752-757; McPherron and Lee, Proc. Natl. Acad. Sci. USA (1997) 94:12457-12461; Kambadur et al. Genome Res. (1997) 7:910-915; and Schuelke et al. (2004) N Engl J Med, 350:2682-8). Studies have also shown that muscle wasting associated with HIV-infection in humans is accompanied by increases in GDF8 protein expression (Gonzalez-Cadavid et al., PNAS (1998) 95:14938-43). In addition, GDF8 can modulate the production of muscle-specific enzymes (e.g., creatine kinase) and modulate myoblast cell proliferation [International Patent Application Publication No. WO 00/43781]. The GDF8 propeptide can noncovalently bind to the processed GDF8 domain dimer, inactivating its biological activity [Miyazono et al. (1988) J. Biol. Chem., 263: 6407-6415; Wakefield et al. (1988) J. Biol. Chem., 263; 7646-7654; and Brown et al. (1990) Growth Factors, 3: 35-43]. Other proteins which bind to GDF8 or structurally related proteins and inhibit their biological activity include follistatin, and potentially, follistatin-related proteins [Gamer et al. (1999) Dev. Biol., 208: 222-232].

GDF11, also known as BMP11, is a secreted protein that is expressed in the tail bud, limb bud, maxillary and mandibular arches, and dorsal root ganglia during mouse development [McPherron et al. (1999) Nat. Genet., 22: 260-264; and Nakashima et al. (1999) Mech. Dev., 80: 185-189]. GDF11 plays a unique role in patterning both mesodermal and neural tissues [Gamer et al. (1999) Dev Biol., 208:222-32]. GDF11 was shown to be a negative regulator of chondrogenesis and myogenesis in developing chick limb [Gamer et al. (2001) Dev Biol., 229:407-20]. The expression of GDF11 in muscle also suggests its role in regulating muscle growth in a similar way to GDF8. In addition, the expression of GDF11 in brain suggests that GDF11 may also possess activities that relate to the function of the nervous system. Interestingly, GDF11 was found to inhibit neurogenesis in the olfactory epithelium [Wu et al. (2003) Neuron., 37:197-207]. Hence, GDF11 may have in vitro and in vivo applications in the treatment of diseases such as muscle diseases and neurodegenerative diseases (e.g., amyotrophic lateral sclerosis).

In part, the disclosure relates to the discovery that activin and/or GDF antagonists (inhibitors) treat or reduce the progression rate and/or severity of kidney disease, particularly treating, preventing or reducing the progression rate and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation). In some embodiments, the disclosure relates to the use of activin and/or GDF antagonists that inhibit one or more of activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF11, GDF8, GDF3, GDF1, Nodal, ALK4, ALK5, ALK7, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3, etc.) for use in treating, preventing, or reducing the progression rate and/or severity of kidney disease or treating, preventing, or reducing the progression rate, frequency, and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

The terms used in this specification generally have their ordinary meanings in the art, within the context of this disclosure and in the specific context where each term is used. Certain terms are discussed below or elsewhere in the specification to provide additional guidance to the practitioner in describing the compositions and methods of the disclosure and how to make and use them. The scope or meaning of any use of a term will be apparent from the specific context in which it is used.

“Homologous,” in all its grammatical forms and spelling variations, refers to the relationship between two proteins that possess a “common evolutionary origin,” including proteins from superfamilies in the same species of organism, as well as homologous proteins from different species of organism. Such proteins (and their encoding nucleic acids) have sequence homology, as reflected by their sequence similarity, whether in terms of percent identity or by the presence of specific residues or motifs and conserved positions. However, in common usage and in the instant application, the term “homologous,” when modified with an adverb such as “highly,” may refer to sequence similarity and may or may not relate to a common evolutionary origin.

The term “sequence similarity,” in all its grammatical forms, refers to the degree of identity or correspondence between nucleic acid or amino acid sequences that may or may not share a common evolutionary origin.

“Percent (%) sequence identity” with respect to a reference polypeptide (or nucleotide) sequence is defined as the percentage of amino acid residues (or nucleic acids) in a candidate sequence that are identical to the amino acid residues (or nucleic acids) in the reference polypeptide (nucleotide) sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid (nucleic acid) sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif., or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.

“Agonize”, in all its grammatical forms, refers to the process of activating a protein and/or gene (e.g., by activating or amplifying that protein's gene expression or by inducing an inactive protein to enter an active state) or increasing a protein's and/or gene's activity.

“Antagonize”, in all its grammatical forms, refers to the process of inhibiting a protein and/or gene (e.g., by inhibiting or decreasing that protein's gene expression or by inducing an active protein to enter an inactive state) or decreasing a protein's and/or gene's activity.

The terms “about” and “approximately” as used in connection with a numerical value throughout the specification and the claims denotes an interval of accuracy, familiar and acceptable to a person skilled in the art. In general, such interval of accuracy is ±10%. Alternatively, and particularly in biological systems, the terms “about” and “approximately” may mean values that are within an order of magnitude, preferably ≤5-fold and more preferably ≤2-fold of a given value.

Numeric ranges disclosed herein are inclusive of the numbers defining the ranges.

The terms “a” and “an” include plural referents unless the context in which the term is used clearly dictates otherwise. The terms “a” (or “an”), as well as the terms “one or more,” and “at least one” can be used interchangeably herein. Furthermore, “and/or” where used herein is to be taken as specific disclosure of each of the two or more specified features or components with or without the other. Thus, the term “and/or” as used in a phrase such as “A and/or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

Throughout this specification, the word “comprise” or variations such as “comprises” or “comprising” will be understood to imply the inclusion of a stated integer or groups of integers but not the exclusion of any other integer or group of integers.

2. TGF-Beta Superfamily Type I Receptor, Type II Receptor, and Co-Receptor Polypeptides, Variants Thereof, and Protein Complexes

In certain aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses disclosed herein is an ActRII polypeptide (e.g., an ActRIIA or ActRIIB polypeptide), variant thereof, or a protein complex comprising at least one ActRII polypeptide (e.g., a homodimer comprising two ActRII polypeptides or a heterodimer comprising one ActRII polypeptide and a heterologous polypeptide (e.g., ALK4)). As used herein, the term “ActRII” refers to the family of type II activin receptors. This family includes activin receptor type IIA (ActRIIA) and activin receptor type IIB (ActRIIB) An ActRII polypeptide, or protein complex comprising an ActRII polypeptide, may inhibit, for example, one or more ActRII-binding ligands (e.g., activin, GDF8, GDF11, GDF3, GDF1 and Nodal), ActRII receptor (e.g., ActRIIA and ActRIIB), ActRII-associated type I receptor (e.g., ALK4, ALK5, ALK7, etc.), and/or ActRII-associated co-receptor (e.g, Cripto, Cryptic, Cryptic 1B, etc.). In some embodiments, the ability for an ActRII polypeptide, or protein complex comprising an ActRII polypeptide, to inhibit signaling (e.g., Smad signaling) is determined in a cell-based assay including, for example, those described herein. An ActRII polypeptide, or protein complex comprising an ActRII polypeptide, may be used alone or in combination with one or more additional supportive therapies or active agents to treat, prevent, or reduce the progression rate and/or severity of kidney disease or one or more complications of kidney disease.

As used herein, the term “ActRIIB” refers to a family of activin receptor type IIB (ActRIIB) proteins from any species and variants derived from such ActRIIB proteins by mutagenesis or other modification. Reference to ActRIIB herein is understood to be a reference to any one of the currently identified forms. Members of the ActRIIB family are generally transmembrane proteins, composed of a ligand-binding extracellular domain comprising a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ActRIIB polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ActRIIB family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Examples of such variant ActRIIB polypeptides are provided throughout the present disclosure as well as in International Patent Application Publication Nos. WO 2006/012627, WO 2008/097541, WO 2010/151426, and WO 2011/020045, which are incorporated herein by reference in their entirety. Numbering of amino acids for all ActRIIB-related polypeptides described herein is based on the numbering of the human ActRIIB precursor protein sequence (SEQ ID NO: 1; NCBI database accession No. NP_001097.2), unless specifically designated otherwise. Another ActRIIB mutant containing an arginine-to-alanine substitution at position 64 is showing in SEQ ID NO: 2.

A processed extracellular ActRIIB polypeptide sequence is set forth in SEQ ID NO: 3. A processed extracellular ActRIIB polypeptide sequence of the alternative A64 form is set forth in SEQ ID NO: 4. The C-terminal “tail” of the extracellular domain is indicated by single underline in both sequences.

In some embodiments, the protein may be produced with an “SGR . . . ” sequence at the N-terminus. The sequence with the “tail” deleted (a Δ15 sequence) is set forth in SEQ ID NOs: 5 and 6, representing the wild type and a R64A mutant, respectively.

A nucleic acid sequence encoding the human ActRIIB precursor protein is shown as SEQ ID NO: 7, representing nucleotides 25-1560 of Genbank Reference Sequence NM_001106.3, which encode amino acids 1-513 of the ActRIIB precursor. The sequence as shown provides an arginine at position 64 and may be modified to provide an alanine instead. The signal sequence is underlined.

A nucleic acid sequence encoding processed extracellular human ActRIIB polypeptide (SEQ ID NO: 3) is set forth in SEQ ID NO: 8. The codon for arginine at position 64 of this sequence may be replaced by a codon for an alanine instead.

An alignment of the amino acid sequences of human ActRIIB extracellular domain and human ActRIIA extracellular domain are illustrated in FIG. 1. This alignment indicates amino acid residues within both receptors that are believed to directly contact ActRII ligands. For example, the composite ActRII structures indicated that the ActRIIB-ligand binding pocket is defined, in part, by residues Y31, N33, N35, L38 through T41, E47, E50, Q53 through K55, L57, H58, Y60, S62, K74, W78 through N83, Y85, R87, A92, and E94 through F101. At these positions, it is expected that conservative mutations will be tolerated.

In addition, ActRIIB is well-conserved among vertebrates, with large stretches of the extracellular domain completely conserved. For example, FIG. 2 depicts a multi-sequence alignment of a human ActRIIB extracellular domain compared to various ActRIIB orthologs. Many of the ligands that bind to ActRIIB are also highly conserved. Accordingly, from these alignments, it is possible to predict key amino acid positions within the ligand-binding domain that are important for normal ActRIIB-ligand binding activities as well as to predict amino acid positions that are likely to be tolerant to substitution without significantly altering normal ActRIIB-ligand binding activities. Therefore, an active, human ActRIIB variant polypeptide useful in accordance with the presently disclosed methods may include one or more amino acids at corresponding positions from the sequence of another vertebrate ActRIIB, or may include a residue that is similar to that in the human or other vertebrate sequences. Without meaning to be limiting, the following examples illustrate this approach to defining an active ActRIIB variant. L46 in the human extracellular domain is a valine in Xenopus ActRIIB, and so this position may be altered, and optionally may be altered to another hydrophobic residue, such as V, I or F, or a non-polar residue such as A. E52 in the human extracellular domain is a K in Xenopus, indicating that this site may be tolerant of a wide variety of changes, including polar residues, such as E, D, K, R, H, S, T, P, G, Y and probably A. T93 in the human extracellular domain is a K in Xenopus, indicating that a wide structural variation is tolerated at this position, with polar residues favored, such as S, K, R, E, D, H, G, P, G and Y. F108 in the human extracellular domain is a Y in Xenopus, and therefore Y or other hydrophobic group, such as I, V or L should be tolerated. E111 in the human extracellular domain is K in Xenopus, indicating that charged residues will be tolerated at this position, including D, R, K and H, as well as Q and N. R112 in the human extracellular domain is K in Xenopus, indicating that basic residues are tolerated at this position, including R and H. A at position 119 in the human extracellular domain is relatively poorly conserved, and appears as P in rodents and V in Xenopus, thus essentially any amino acid should be tolerated at this position.

Moreover, ActRII proteins have been characterized in the art in terms of structural and functional characteristics, particularly with respect to ligand binding [Attisano et al. (1992) Cell 68(1):97-108; Greenwald et al. (1999) Nature Structural Biology 6(1): 18-22; Allendorph et al. (2006) PNAS 103(20: 7643-7648; Thompson et al. (2003) The EMBO Journal 22(7): 1555-1566; as well as U.S. Pat. Nos. 7,709,605, 7,612,041, and 7,842,663]. In addition to the teachings herein, these references provide ample guidance for how to generate ActRIIB variants that retain one or more normal activities (e.g., ligand-binding activity).

For example, a defining structural motif known as a three-finger toxin fold is important for ligand binding by type I and type II receptors and is formed by conserved cysteine residues located at varying positions within the extracellular domain of each monomeric receptor (Greenwald et al. (1999) Nat Struct Biol 6:18-22; and Hinck (2012) FEBS Lett 586:1860-1870). Accordingly, the core ligand-binding domains of human ActRIIB, as demarcated by the outermost of these conserved cysteines, corresponds to positions 29-109 of SEQ ID NO: 1 (ActRIIB precursor). The structurally less-ordered amino acids flanking these cysteine-demarcated core sequences can be truncated by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 residues at the N-terminus and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 residues at the C-terminus without necessarily altering ligand binding. Exemplary ActRIIB extracellular domains for N-terminal and/or C-terminal truncation include SEQ ID NOs: 3, 4, 5, and 6.

Attisano et al. showed that a deletion of the proline knot at the C-terminus of the extracellular domain of ActRIIB reduced the affinity of the receptor for activin. An ActRIIB-Fc fusion protein containing amino acids 20-119 of present SEQ ID NO: 1, “ActRIIB(20-119)-Fc”, has reduced binding to GDF11 and activin relative to an ActRIIB(20-134)-Fc, which includes the proline knot region and the complete juxtamembrane domain (see, e.g., U.S. Pat. No. 7,842,663). However, an ActRIIB(20-129)-Fc protein retains similar, but somewhat reduced activity, relative to the wild-type, even though the proline knot region is disrupted.

Thus, ActRIIB extracellular domains that stop at amino acid 134, 133, 132, 131, 130 and 129 (with respect to SEQ ID NO: 1) are all expected to be active, but constructs stopping at 134 or 133 may be most active. Similarly, mutations at any of residues 129-134 (with respect to SEQ ID NO: 1) are not expected to alter ligand-binding affinity by large margins. In support of this, it is known in the art that mutations of P129 and P130 (with respect to SEQ ID NO: 1) do not substantially decrease ligand binding. Therefore, an ActRIIB polypeptide of the present disclosure may end as early as amino acid 109 (the final cysteine), however, forms ending at or between 109 and 119 (e.g., 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, or 119) are expected to have reduced ligand binding. Amino acid 119 (with respect to present SEQ ID NO:1) is poorly conserved and so is readily altered or truncated. ActRIIB polypeptides ending at 128 (with respect to SEQ ID NO: 1) or later should retain ligand-binding activity. ActRIIB polypeptides ending at or between 119 and 127 (e.g., 119, 120, 121, 122, 123, 124, 125, 126, or 127), with respect to SEQ ID NO: 1, will have an intermediate binding ability. Any of these forms may be desirable to use, depending on the clinical or experimental setting.

At the N-terminus of ActRIIB, it is expected that a protein beginning at amino acid 29 or before (with respect to SEQ ID NO: 1) will retain ligand-binding activity. Amino acid 29 represents the initial cysteine. An alanine-to-asparagine mutation at position 24 (with respect to SEQ ID NO: 1) introduces an N-linked glycosylation sequence without substantially affecting ligand binding (U.S. Pat. No. 7,842,663). This confirms that mutations in the region between the signal cleavage peptide and the cysteine cross-linked region, corresponding to amino acids 20-29, are well tolerated. In particular, ActRIIB polypeptides beginning at position 20, 21, 22, 23, and 24 (with respect to SEQ ID NO: 1) should retain general ligand-biding activity, and ActRIIB polypeptides beginning at positions 25, 26, 27, 28, and 29 (with respect to SEQ ID NO: 1) are also expected to retain ligand-biding activity. It has been demonstrated, e.g., U.S. Pat. No. 7,842,663, that, surprisingly, an ActRIIB construct beginning at 22, 23, 24, or 25 will have the most activity.

Taken together, a general formula for an active portion (e.g., ligand-binding portion) of ActRIIB comprises amino acids 29-109 of SEQ ID NO: 1. Therefore ActRIIB polypeptides may, for example, comprise, consist essentially of, or consist of an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIB beginning at a residue corresponding to any one of amino acids 20-29 (e.g., beginning at any one of amino acids 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) of SEQ ID NO: 1 and ending at a position corresponding to any one amino acids 109-134 (e.g., ending at any one of amino acids 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134) of SEQ ID NO: 1. Other examples include polypeptides that begin at a position from 20-29 (e.g., any one of positions 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29) or 21-29 (e.g., any one of positions 21, 22, 23, 24, 25, 26, 27, 28, or 29) of SEQ ID NO: 1 and end at a position from 119-134 (e.g., any one of positions 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134), 119-133 (e.g., any one of positions 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, or 133), 129-134 (e.g., any one of positions 129, 130, 131, 132, 133, or 134), or 129-133 (e.g., any one of positions 129, 130, 131, 132, or 133) of SEQ ID NO: 1. Other examples include constructs that begin at a position from 20-24 (e.g., any one of positions 20, 21, 22, 23, or 24), 21-24 (e.g., any one of positions 21, 22, 23, or 24), or 22-25 (e.g., any one of positions 22, 22, 23, or 25) of SEQ ID NO: 1 and end at a position from 109-134 (e.g., any one of positions 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134), 119-134 (e.g., any one of positions 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, or 134) or 129-134 (e.g., any one of positions 129, 130, 131, 132, 133, or 134) of SEQ ID NO: 1. Variants within these ranges are also contemplated, particularly those comprising, consisting essentially of, or consisting of an amino acid sequence that has at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the corresponding portion of SEQ ID NO: 1.

The variations described herein may be combined in various ways. In some embodiments, ActRIIB variants comprise no more than 1, 2, 5, 6, 7, 8, 9, 10 or 15 conservative amino acid changes in the ligand-binding pocket, optionally zero, one or more non-conservative alterations at positions 40, 53, 55, 74, 79 and/or 82 in the ligand-binding pocket. Sites outside the binding pocket, at which variability may be particularly well tolerated, include the amino and carboxy termini of the extracellular domain (as noted above), and positions 42-46 and 65-73 (with respect to SEQ ID NO: 1). An asparagine-to-alanine alteration at position 65 (N65A) does not appear to decrease ligand binding in the R64 background (U.S. Pat. No. 7,842,663). This change probably eliminates glycosylation at N65 in the A64 background, thus demonstrating that a significant change in this region is likely to be tolerated. While an R64A change is poorly tolerated, R64K is well-tolerated, and thus another basic residue, such as H, may be tolerated at position 64 (U.S. Pat. No. 7,842,663). Additionally, the results of the mutagenesis program described in the art indicate that there are amino acid positions in ActRIIB that are often beneficial to conserve. With respect to SEQ ID NO: 1, these include position 80 (acidic or hydrophobic amino acid), position 78 (hydrophobic, and particularly tryptophan), position 37 (acidic, and particularly aspartic or glutamic acid), position 56 (basic amino acid), position 60 (hydrophobic amino acid, particularly phenylalanine or tyrosine). Thus, the disclosure provides a framework of amino acids that may be conserved in ActRIIB polypeptides. Other positions that may be desirable to conserve are as follows: position 52 (acidic amino acid), position 55 (basic amino acid), position 81 (acidic), 98 (polar or charged, particularly E, D, R or K), all with respect to SEQ ID NO: 1.

It has been previously demonstrated that the addition of a further N-linked glycosylation site (N-X-S/T) into the ActRIIB extracellular domain is well-tolerated (see, e.g., U.S. Pat. No. 7,842,663). Therefore, N-X-S/T sequences may be generally introduced at positions outside the ligand binding pocket defined in FIG. 1 in ActRIIB polypeptide of the present disclosure. Particularly suitable sites for the introduction of non-endogenous N-X-S/T sequences include amino acids 20-29, 20-24, 22-25, 109-134, 120-134 or 129-134 (with respect to SEQ ID NO: 1). N-X-S/T sequences may also be introduced into the linker between the ActRIIB sequence and an Fc domain or other fusion component as well as optionally into the fusion component itself. Such a site may be introduced with minimal effort by introducing an N in the correct position with respect to a pre-existing S or T, or by introducing an S or T at a position corresponding to a pre-existing N. Thus, desirable alterations that would create an N-linked glycosylation site are: A24N, R64N, S67N (possibly combined with an N65A alteration), E105N, R112N, G120N, E123N, P129N, A132N, R112S and R112T (with respect to SEQ ID NO: 1). Any S that is predicted to be glycosylated may be altered to a T without creating an immunogenic site, because of the protection afforded by the glycosylation. Likewise, any T that is predicted to be glycosylated may be altered to an S. Thus the alterations S67T and S44T (with respect to SEQ ID NO: 1) are contemplated. Likewise, in an A24N variant, an S26T alteration may be used. Accordingly, an ActRIIB polypeptide of the present disclosure may be a variant having one or more additional, non-endogenous N-linked glycosylation consensus sequences as described above.

In certain aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses disclosed herein is an ActRIIB polypeptide (which includes fragments and functional variants variant thereof) as well as protein complexes comprising at least one ActRIIB polypeptide (e.g., an homodimer comprising two ActRIIB polypeptides or a heterodimer comprising one ActRIIB polypeptide and a heterologous polypeptide (e.g., ALK4)). Preferably, ActRIIB polypeptides are soluble (e.g., comprise an extracellular domain of ActRIIB) In some embodiments, ActRIIB polypeptides antagonize activity (e.g., Smad signaling) of one or more activin and/or GDF ligands (e.g., GDF11, GDF8, activin (activin A, activin B, activin AB, activin C, activin E), GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3). Therefore, in some embodiments, ActRIIB polypeptides bind to one or more activin and/or GDF ligands (e.g., GDF11, GDF8, activin (activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF3, GDF1, Nodal, ActRIIA, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3, etc.)). In some embodiments, ActRIIB polypeptides of the disclosure comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIB beginning at a residue corresponding to amino acids 20-29 of SEQ ID NO: 1 and ending at a position corresponding to amino acids 109-134 of SEQ ID NO: 1. In some embodiments, ActRIIB polypeptides comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical amino acids 29-109 of SEQ ID NO: 1. In certain embodiments, ActRIIB polypeptides of the disclosure comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical amino acids 25-131 of SEQ ID NO: 1. In some embodiments, ActRIIB polypeptide of disclosure comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 181, 182, 184, 187, 188, 189, 190, 192, 193, 196, 197, 198, 199, 201, 205, and 206. In some embodiments, ActRIIB polypeptides of the disclosure comprise an ActRIIB polypeptide wherein the position corresponding to L79 of SEQ ID NO: 1 is not an acidic amino acid (i.e., is not naturally occurring acid amino acids D or E or an artificial acidic amino acid residue).

In certain embodiments, the present disclosure relates to ActRIIA polypeptides. As used herein, the term “ActRIIA” refers to a family of activin receptor type IIA (ActRIIA) proteins from any species and variants derived from such ActRIIA proteins by mutagenesis or other modification. Reference to ActRIIA herein is understood to be a reference to any one of the currently identified forms. Members of the ActRIIA family are generally transmembrane proteins, composed of a ligand-binding extracellular domain comprising a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ActRIIA polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ActRIIA family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Examples of such variant ActRIIA polypeptides are provided throughout the present disclosure as well as in International Patent Application Publication Nos. WO 2006/012627 and WO 2007/062188, which are incorporated herein by reference in their entirety.

The human ActRIIA precursor protein sequence is set forth in SEQ ID NO: 9 or 10.

A processed extracellular human ActRIIA polypeptide sequence is set in SEQ ID NO: 11. A nucleic acid sequence encoding the processed extracellular ActRIIA polypeptide has a sequence of SEQ ID NO: 14.

A sequence having the C-terminal “tail” of the extracellular domain deleted (a Δ15 sequence) is set forth in SEQ ID NO: 12.

A nucleic acid sequence encoding the human ActRIIA precursor protein (SEQ ID NO: 9) is shown below (SEQ ID NO: 13), corresponding to nucleotides 159-1700 of Genbank Reference Sequence NM_001616.4. The signal sequence is underlined.

ActRIIA is well-conserved among vertebrates, with large stretches of the extracellular domain completely conserved. For example, FIG. 3 depicts a multi-sequence alignment of a human ActRIIA extracellular domain compared to various ActRIIA orthologs. Many of the ligands that bind to ActRIIA are also highly conserved. Accordingly, from these alignments, it is possible to predict key amino acid positions within the ligand-binding domain that are important for normal ActRIIA-ligand binding activities as well as to predict amino acid positions that are likely to be tolerant to substitution without significantly altering normal ActRIIA-ligand binding activities. Therefore, an active, human ActRIIA variant polypeptide useful in accordance with the presently disclosed methods may include one or more amino acids at corresponding positions from the sequence of another vertebrate ActRIIA, or may include a residue that is similar to that in the human or other vertebrate sequences.

Without meaning to be limiting, the following examples illustrate this approach to defining an active ActRIIA variant. As illustrated in FIG. 3, F13 in the human extracellular domain is Y in Ovis aries (SEQ ID NO: 18), Gallus gallus (SEQ ID NO: 21), Bos taurus (SEQ ID NO: 22), Tyto alba (SEQ ID NO: 23), and Myotis davidii (SEQ ID NO: 24) ActRIIA, indicating that aromatic residues are tolerated at this position, including F, W, and Y. Q24 in the human extracellular domain is R in Bos taurus ActRIIA, indicating that charged residues will be tolerated at this position, including D, R, K, H, and E. S95 in the human extracellular domain is F in Gallus gallus and Tyto alba ActRIIA, indicating that this site may be tolerant of a wide variety of changes, including polar residues, such as E, D, K, R, H, S, T, P, G, Y, and probably hydrophobic residue such as L, I, or F. E52 in the human extracellular domain is D in Ovis aries ActRIIA, indicating that acidic residues are tolerated at this position, including D and E. P29 in the human extracellular domain is relatively poorly conserved, appearing as S in Ovis aries ActRIIA and L in Myotis davidii ActRIIA, thus essentially any amino acid should be tolerated at this position.

Moreover, as discussed above, ActRII proteins have been characterized in the art in terms of structural/functional characteristics, particularly with respect to ligand binding [Attisano et al. (1992) Cell 68(1):97-108; Greenwald et al. (1999) Nature Structural Biology 6(1): 18-22; Allendorph et al. (2006) PNAS 103(20: 7643-7648; Thompson et al. (2003) The EMBO Journal 22(7): 1555-1566; as well as U.S. Pat. Nos: 7,709,605, 7,612,041, and 7,842,663]. In addition to the teachings herein, these references provide amply guidance for how to generate ActRII variants that retain one or more desired activities (e.g., ligand-binding activity).

For example, a defining structural motif known as a three-finger toxin fold is important for ligand binding by type I and type II receptors and is formed by conserved cysteine residues located at varying positions within the extracellular domain of each monomeric receptor [Greenwald et al. (1999) Nat Struct Biol 6:18-22; and Hinck (2012) FEBS Lett 586:1860-1870]. Accordingly, the core ligand-binding domains of human ActRIIA, as demarcated by the outermost of these conserved cysteines, corresponds to positions 30-110 of SEQ ID NO: 9 (ActRIIA precursor). Therefore, the structurally less-ordered amino acids flanking these cysteine-demarcated core sequences can be truncated by about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 residues at the N-terminus and by about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 residues at the C-terminus without necessarily altering ligand binding. Exemplary ActRIIA extracellular domains truncations include SEQ ID NO: 12.

Accordingly, a general formula for an active portion (e.g., ligand binding) of ActRIIA is a polypeptide that comprises, consists essentially of, or consists of amino acids 30-110 of SEQ ID NO: 9. Therefore ActRIIA polypeptides may, for example, comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIA beginning at a residue corresponding to any one of amino acids 21-30 of SEQ ID NO: 9 and ending at a position corresponding to any one amino acids 110-135 of SEQ ID NO: 9. Other examples include constructs that begin at a position selected from 21-30, 22-30, 23-30, 24-30 of SEQ ID NO: 9, and end at a position selected from 111-135, 112-135, 113-135, 120-135,130-135, 111-134, 111-133, 111-132, or 111-131 of SEQ ID NO: 9. Variants within these ranges are also contemplated, particularly those comprising an amino acid sequence that has at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the corresponding portion of SEQ ID NO: 9. Thus, in some embodiments, an ActRIIA polypeptide may comprise a polypeptide that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids 30-110 of SEQ ID NO: 9. Optionally, ActRIIA polypeptides comprise a polypeptide that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids 30-110 of SEQ ID NO: 9, and comprising no more than 1, 2, 5, 10 or 15 conservative amino acid changes in the ligand-binding pocket.

In certain aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses disclosed herein is an ActRIIA polypeptide (which includes fragments and functional variants variant thereof) or a protein complex comprising at least one ActRIIA polypeptide (e.g., an homodimer comprising two ActRIIA polypeptides or a heterodimer comprising one ActRIIA polypeptide and a heterologous polypeptide (e.g., ALK4)). Preferably, ActRIIA polypeptides are soluble (e.g., an extracellular domain of ActRIIA). In some embodiments, ActRIIA polypeptides inhibit (e.g., Smad signaling) of one or more activin and/or GDF ligands (e.g., GDF11, GDF8, activin (activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF3, GDF1, Nodal, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3, etc.). In some embodiments, ActRIIA polypeptides bind to one or more activin and/or GDF ligands (e.g., GDF11, GDF8, activin (activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF3, GDF1, Nodal, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3, etc.)). In some embodiments, ActRIIA polypeptide of the disclosure comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a portion of ActRIIA beginning at a residue corresponding to amino acids 21-30 of SEQ ID NO: 9 and ending at a position corresponding to any one amino acids 110-135 of SEQ ID NO: 9. In some embodiments, ActRIIA polypeptides comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical amino acids 30-110 of SEQ ID NO: 9. In certain embodiments, ActRIIA polypeptides comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical amino acids 21-135 of SEQ ID NO: 9. In some embodiments, ActRIIA polypeptides comprise an amino acid sequence that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any one of SEQ ID NOs: 9, 10, 11, 12, 15, 18-24, 177, 178, and 180.

In certain aspects, the present disclosure relates to heteromultimers that comprise a BMPRII polypeptide. As used herein, the term “BMPRII” refers to a family of bone morphogenetic protein receptor type II (BMPRII) proteins from any species and variants derived from such BMPRII proteins by mutagenesis or other modification. Reference to BMPRII herein is understood to be a reference to any one of the currently identified forms. Members of the BMPRII family are generally transmembrane proteins, having a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “BMPRII polypeptide” includes polypeptides comprising any naturally occurring polypeptide of a BMPRII family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all BMPRII-related polypeptides described herein is based on the numbering of the human BMPRII precursor protein sequence (SEQ ID NO: 34, NCBI Ref Seq NP_001195.2), unless specifically designated otherwise. In SEQ ID NO: 34, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding BMPRII precursor protein is shown in SEQ ID NO: 35, as nucleotides 1149-4262 of Genbank Reference Sequence NM_001204.6. A processed extracellular BMPRII polypeptide sequence is set forth in SEQ ID NO: 36, which is encodable by a nucleic acid sequence of SEQ ID NO: 37. An alternative isoform of BMPRII, isoform 2 (GenBank: AAA86519.1) is set forth in SEQ ID NO: 38 (the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font), which is encodable by a nucleic acid sequence of SEQ ID NO: 39 (corresponding to nucleotides 163-1752 of Genbank Reference Sequence U25110.1, the signal sequence is underlined). A processed extracellular BMPRII polypeptide sequence (isoform 2) is set forth in SEQ ID NO: 40, which is encodable by a nucleic acid sequence of SEQ ID NO: 41.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, BMPRII polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising a BMPRII polypeptide and uses thereof) are soluble (e.g., an extracellular domain of BMPRII). In other preferred embodiments, BMPRII polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 34, 36, 38, or 40. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 27-34 (e.g., amino acid residues 27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 34, and ends at any one of amino acids 123-150 (e.g., amino acid residues 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, or 150) of SEQ ID NO: 34. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 27-123 of SEQ ID NO: 34. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 27-150 of SEQ ID NO: 34. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-123 of SEQ ID NO: 34. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-150 of SEQ ID NO: 34. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 27-34 (e.g., amino acid residues 27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 38, and ends at any one of amino acids 123-150 (e.g., amino acid residues 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, or 150) of SEQ ID NO: 38. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 27-123 of SEQ ID NO: 38. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 27-150 of SEQ ID NO: 38. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-123 of SEQ ID NO: 38. In some embodiments, heteromultimers of the disclosure comprise at least one BMPRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-150 of SEQ ID NO: 38.

In certain aspects, the present disclosure relates to heteromultimers that comprise an MISRII polypeptide. As used herein, the term “MISRII” refers to a family of Müllerian inhibiting substance receptor type II (MISRII) proteins from any species and variants derived from such MISRII proteins by mutagenesis or other modification. Reference to MISRII herein is understood to be a reference to any one of the currently identified forms. Members of the MISRII family are generally transmembrane proteins, composed of a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “MISRII polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an MISRII family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all MISRII-related polypeptides described herein is based on the numbering of the human MISRII precursor protein sequence (SEQ ID NO: 42, NCBI Ref Seq NP_065434.1), unless specifically designated otherwise. In SEQ ID NO: 42, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding the MISRII precursor protein is shown in SEQ ID NO: 43, corresponding to nucleotides 81-1799 of Genbank Reference Sequence NM_020547.2. A processed extracellular MISRII polypeptide sequence (isoform 1) is set forth in SEQ ID NO: 44, which is encodable by a nucleic acid sequence of SEQ ID NO: 45. An alternative isoform of the human MISRII precursor protein sequence, isoform 2 (NCBI Ref Seq NP_001158162.1), is set forth in SEQ ID NO: 46 (the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font), which is encodable by a nucleic acid sequence of SEQ ID NO: 47, corresponding to nucleotides 81-1514 of Genbank Reference Sequence NM_001164690.1. A processed extracellular MISRII polypeptide sequence (isoform 2) is 100% identical to the corresponding processed extracellular MISRII polypeptide sequence (isoform 1) (i.e., having an amino acid sequence of SEQ ID NO: 44, which is encodable by a nucleic acid sequence of SEQ ID NO: 45). An alternative isoform of the human MISRII precursor protein sequence, isoform 3 (NCBI Ref Seq NP_001158163.1), is set forth in SEQ ID NO: 48 (the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font), which is encodable by a nucleic acid sequence of SEQ ID NO: 49, corresponding to nucleotides 81-1514 of Genbank Reference Sequence NM_001164691.1. The signal sequence is underlined. A processed extracellular MISRII polypeptide sequence (isoform 3) is 100% identical to the corresponding processed extracellular MISRII polypeptide sequence (isoform 1) (i.e., having an amino acid sequence of SEQ ID NO: 44, which is encodable by a nucleic acid sequence of SEQ ID NO: 45).

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, MISRII polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising a MISRII polypeptide and uses thereof) are soluble (e.g., an extracellular domain of MISRII). In other preferred embodiments, MISRII polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 42, 44, 46, or 48. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 17-24 (e.g., amino acid residues 17, 18, 19, 20, 21, 22, 23, or 24) of SEQ ID NO: 42, and ends at any one of amino acids 116-149 (e.g., amino acid residues 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, or 149) of SEQ ID NO: 42. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-116 of SEQ ID NO: 42. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-149 of SEQ ID NO: 42. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-116 of SEQ ID NO: 42. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-149 of SEQ ID NO: 42. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 17-24 (e.g., amino acid residues 17, 18, 19, 20, 21, 22, 23, or 24) of SEQ ID NO: 46, and ends at any one of amino acids 116-149 (e.g., amino acid residues 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, or 149) of SEQ ID NO: 46. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-116 of SEQ ID NO: 46. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-149 of SEQ ID NO: 46. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-116 of SEQ ID NO: 46. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-149 of SEQ ID NO: 46. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 17-24 (e.g., amino acid residues 17, 18, 19, 20, 21, 22, 23, or 24) of SEQ ID NO: 42, and ends at any one of amino acids 116-149 (e.g., amino acid residues 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, or 149) of SEQ ID NO: 48. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-116 of SEQ ID NO: 48. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 17-149 of SEQ ID NO: 48. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-116 of SEQ ID NO: 48. In some embodiments, heteromultimers of the disclosure comprise at least one MISRII polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-149 of SEQ ID NO: 48.

In certain aspects, the present disclosure relates to heteromultimers that comprise an ALK1 polypeptide. As used herein, the term “ALK1” refers to a family of activin receptor-like kinase-1 proteins from any species and variants derived from such ALK1 proteins by mutagenesis or other modification. Reference to ALK1 herein is understood to be a reference to any one of the currently identified forms. Members of the ALK1 family are generally transmembrane proteins, composed of a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ALK1 polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ALK1 family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all ALK1-related polypeptides described herein is based on the numbering of the human ALK1 precursor protein sequence (SEQ ID NO: 52, NCBI Ref Seq NP_000011.2), unless specifically designated otherwise. In SEQ ID NO: 52, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding human ALK1 precursor protein is set forth in SEQ ID NO: 53, corresponding to nucleotides 284-1792 of Genbank Reference Sequence NM_000020.2. A processed extracellular ALK1 polypeptide sequence is set forth in SEQ ID NO: 54, which is encodable by a nucleic acid sequence of SEQ ID NO: 55.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, ALK1 polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising an ALK1 polypeptide and uses thereof) are soluble (e.g., an extracellular domain of ALK1). In other preferred embodiments, ALK1 polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 52 or 54. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 22-34 (e.g., amino acid residues 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 52, and ends at any one of amino acids 95-118 (e.g., amino acid residues 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, or 119) of SEQ ID NO: 52. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 22-95 of SEQ ID NO: 52. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 22-118 of SEQ ID NO: 52. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-95 of SEQ ID NO: 52. In some embodiments, heteromultimers of the disclosure comprise at least one ALK1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-118 of SEQ ID NO: 52.

In certain aspects, the present disclosure relates to heteromultimers that comprise an ALK4 polypeptide. As used herein, the term “ALK4” refers to a family of activin receptor-like kinase-4 proteins from any species and variants derived from such ALK4 proteins by mutagenesis or other modification. Reference to ALK4 herein is understood to be a reference to any one of the currently identified forms. Members of the ALK4 family are generally transmembrane proteins, composed of a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ALK4 polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ALK4 family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all ALK4-related polypeptides described herein is based on the numbering of the human ALK4 precursor protein sequence (SEQ ID NO: 56, NCBI Ref Seq NP_004293), unless specifically designated otherwise. In SEQ ID NO: 56, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding the ALK4 precursor protein is set forth in SEQ ID NO: 57, corresponding to nucleotides 78-1592 of Genbank Reference Sequence NM_004302.4. The signal sequence is underlined and the extracellular domain is indicated in bold font. A processed extracellular human ALK4 polypeptide sequence is set forth in SEQ ID NO: 58, which is encodable by a nucleic acid sequence of SEQ ID NO: 59. An alternative isoform of human ALK4 precursor protein sequence, isoform C (NCBI Ref Seq NP_064733.3) is set forth in SEQ ID NO: 60, where the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding the ALK4 precursor protein (isoform C) is set forth in SEQ ID NO: 61, corresponding to nucleotides 78-1715 of Genbank Reference Sequence NM_020328.3. A processed extracellular ALK4 polypeptide sequence (isoform C) is 100% identical to the corresponding processed extracellular ALK4 polypeptide sequence (i.e., having an amino acid sequence of SEQ ID NO: 58, which is encodable by a nucleic acid sequence of SEQ ID NO: 59).

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, ALK4 polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising an ALK4 polypeptide and uses thereof) are soluble (e.g., an extracellular domain of ALK4). In other preferred embodiments, ALK4 polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 56, 58 or 60. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 24-34 (e.g., amino acid residues 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 56, and ends at any one of amino acids 101-126 (e.g., amino acid residues 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, or 126) of SEQ ID NO: 56. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-101 of SEQ ID NO: 56. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-126 of SEQ ID NO: 56. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-101 of SEQ ID NO: 56. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-126 of SEQ ID NO: 56. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 24-34 (e.g., amino acid residues 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34) of SEQ ID NO: 83, and ends at any one of amino acids 101-126 (e.g., amino acid residues 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, or 126) of SEQ ID NO: 60. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-101 of SEQ ID NO: 60. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 24-126 of SEQ ID NO: 60. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-101 of SEQ ID NO: 60. In some embodiments, heteromultimers of the disclosure comprise at least one ALK4 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 34-126 of SEQ ID NO: 60.

In certain aspects, the present disclosure relates to heteromultimers that comprise an ALK5 polypeptide. As used herein, the term “ALK5” refers to a family of activin receptor-like kinase-5 proteins from any species and variants derived from such ALK5 proteins by mutagenesis or other modification. Reference to ALK5 herein is understood to be a reference to any one of the currently identified forms. Members of the ALK5 family are generally transmembrane proteins, having a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ALK5 polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ALK5 family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all ALK5-related polypeptides described herein is based on the numbering of the human ALK5 precursor protein sequence (SEQ ID NO: 62, NCBI Ref Seq NP_004603.1), unless specifically designated otherwise. In SEQ ID NO: 62, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding the ALK5 precursor protein is set forth in SEQ ID NO: 63, corresponding to nucleotides 77-1585 of Genbank Reference Sequence NM_004612.2. A processed extracellular ALK5 polypeptide sequence is set forth in SEQ ID NO: 64, which is encodable by a nucleic acid sequence of SEQ ID NO: 65. An alternative isoform of the human ALK5 precursor protein sequence, isoform 2 (NCBI Ref Seq XP_005252207.1), is set forth in SEQ ID NO: 66 (the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font). A nucleic acid sequence encoding human ALK5 precursor protein (isoform 2) is set forth in SEQ ID NO: 67 (the signal sequence is underlined and the extracellular domain is indicated in bold font), corresponding to nucleotides 77-1597 of Genbank Reference Sequence XM_005252150.1. A processed extracellular ALK5 polypeptide sequence (isoform 2) is set forth in SEQ ID NO: 68, which is encodable by a nucleic acid sequence of SEQ ID NO: 69.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, ALK5 polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising an ALK5 polypeptide and uses thereof) are soluble (e.g., an extracellular domain of ALK5). In other preferred embodiments, ALK5 polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 62, 64, 66, or 68. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 25-36 (e.g., amino acid residues 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36) of SEQ ID NO: 62, and ends at any one of amino acids 101-126 (e.g., amino acid residues 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, or 126) of SEQ ID NO: 62. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 25-101 of SEQ ID NO: 62. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 25-126 of SEQ ID NO: 62. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 36-101 of SEQ ID NO: 62. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 36-126 of SEQ ID NO: 62. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 25-36 (e.g., amino acid residues 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36) of SEQ ID NO: 66, and ends at any one of amino acids 101-130 (e.g., amino acid residues 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129 or 130) of SEQ ID NO: 66. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 25-101 of SEQ ID NO: 66. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 25-130 of SEQ ID NO: 66. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 36-101 of SEQ ID NO: 66. In some embodiments, heteromultimers of the disclosure comprise at least one ALK5 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 36-130 of SEQ ID NO: 66.

In certain aspects, the present disclosure relates to heteromultimers that comprise an ALK7 polypeptide. As used herein, the term “ALK7” refers to a family of activin receptor-like kinase-7 proteins from any species and variants derived from such ALK7 proteins by mutagenesis or other modification. Reference to ALK7 herein is understood to be a reference to any one of the currently identified forms. Members of the ALK7 family are generally transmembrane proteins, composed of a ligand-binding extracellular domain with a cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine kinase activity.

The term “ALK7 polypeptide” includes polypeptides comprising any naturally occurring polypeptide of an ALK7 family member as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all ALK7-related polypeptides described herein is based on the numbering of the human ALK7 precursor protein sequence (SEQ ID NO: 70, NCBI Ref Seq NP_660302.2), unless specifically designated otherwise. In SEQ ID NO: 70, the signal peptide is indicated by a single underline and the extracellular domain is indicated in bold font. A nucleic acid sequence encoding human ALK7 isoform 1 precursor protein is set forth in SEQ ID NO: 71, corresponding to nucleotides 244-1722 of Genbank Reference Sequence NM_145259.2. A processed extracellular ALK7 isoform 1 polypeptide sequence is set forth in SEQ ID NO: 72, which is encodable by a nucleic acid sequence of SEQ ID NO: 73. The amino acid sequence of an alternative isoform of human ALK7, isoform 2 (NCBI Ref Seq NP_001104501.1), is shown in SEQ ID NO: 74, where the extracellular domain is indicated in bold font. A nucleic acid sequence encoding the processed ALK7 polypeptide (isoform 2) is set forth in SEQ ID NO: 75, corresponding to nucleotides 279-1607 of NCBI Reference Sequence NM_001111031.1. An amino acid sequence of the extracellular ALK7 polypeptide (isoform 2) is set forth in SEQ ID NO: 76, which is encodable by a nucleic acid sequence of SEQ ID NO: 77. An amino acid sequence of an alternative human ALK7 precursor protein, isoform 3 (NCBI Ref Seq NP_001104502.1), is set forth in SEQ ID NO: 78, where the signal peptide is indicated by a single underline. A nucleic acid sequence encoding the unprocessed ALK7 polypeptide precursor protein (isoform 3) is set forth in SEQ ID NO: 79, corresponding to nucleotides 244-1482 of NCBI Reference Sequence NM_001111032.1. The signal sequence is indicated by solid underline. An amino acid sequence of the processed ALK7 polypeptide (isoform 3) is set forth in SEQ ID NO: 80. This isoform lacks a transmembrane domain and is therefore proposed to be soluble in its entirety (Roberts et al., 2003, Biol Reprod 68:1719-1726). N-terminal variants of SEQ ID NO: 80 are predicted as described below. A nucleic acid sequence encoding the processed ALK7 polypeptide (isoform 3) is set forth in SEQ ID NO: 81. An amino acid sequence of an alternative human ALK7 precursor protein, isoform 4 (NCBI Ref Seq NP_001104503.1), is set forth in SEQ ID NO: 82, where the signal peptide is indicated by a single underline. A nucleic acid sequence encoding the unprocessed ALK7 polypeptide precursor protein (isoform 4) is set forth in SEQ ID NO: 83, corresponding to nucleotides 244-1244 of NCBI Reference Sequence NM_001111033.1. The signal sequence is indicated by solid underline. An amino acid sequence of the processed ALK7 polypeptide (isoform 4) is set forth in SEQ ID NO: 84. Like ALK7 isoform 3, isoform 4 lacks a transmembrane domain and is therefore proposed to be soluble in its entirety (Roberts et al., 2003, Biol Reprod 68:1719-1726). A nucleic acid sequence encoding the processed ALK7 polypeptide (isoform 4) is set forth in SEQ ID NO: 85.

Based on the signal sequence of full-length ALK7 (isoform 1) in the rat (see NCBI Reference Sequence NP_620790.1) and on the high degree of sequence identity between human and rat ALK7, it is predicted that a processed form of human ALK7 isoform 1 is set forth in SEQ ID NO: 86.

Active variants of processed ALK7 isoform 1 are predicted in which SEQ ID NO: 72 is truncated by 1, 2, 3, 4, 5, 6, or 7 amino acids at the N-terminus and SEQ ID NO: 86 is truncated by 1 or 2 amino acids at the N-terminus. Consistent with SEQ ID NO: 86, it is further expected that leucine is the N-terminal amino acid in the processed forms of human ALK7 isoform 3 (SEQ ID NO: 80) and human ALK7 isoform 4 (SEQ ID NO: 84). In certain embodiments, the disclosure relates to heteromultimers that comprise at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, ALK7 polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising an ALK7 polypeptide and uses thereof) are soluble (e.g., an extracellular domain of ALK7). In other preferred embodiments, ALK7 polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 70, 72, 74, 76, 78, 80, 82, 84, or 86. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 21-28 (e.g., amino acid residues 21, 22, 23, 24, 25, 26, 27, or 28) of SEQ ID NO: 70, and ends at any one of amino acids 92-113 (e.g., amino acid residues 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, or 113) of SEQ ID NO: 70. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-92 of SEQ ID NO: 70. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-113 of SEQ ID NO: 70. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-92 of SEQ ID NO: 70. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-113 of SEQ ID NO: 70. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 1-13 (e.g., amino acid residues 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13) of SEQ ID NO: 74, and ends at any one of amino acids 42-63 (e.g., amino acid residues 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, or 63) of SEQ ID NO: 74. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 1-42 of SEQ ID NO: 74. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 1-63 of SEQ ID NO: 74. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 13-42 of SEQ ID NO: 74. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 13-63 of SEQ ID NO: 74. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 21-28 (e.g., amino acid residues 21, 22, 23, 24, 25, 26, 27, or 28) of SEQ ID NO: 78, and ends at any one of amino acids 411-413 (e.g., amino acid residues 411, 412, or 413) of SEQ ID NO: 78. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-411 of SEQ ID NO: 78. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-413 of SEQ ID NO: 78. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-411of SEQ ID NO: 78. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-413 of SEQ ID NO: 78. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 21-28 (e.g., amino acid residues 21, 22, 23, 24, 25, 26, 27, or 28) of SEQ ID NO: 82, and ends at any one of amino acids 334-336 (e.g., amino acid residues 334, 335, or 336) of SEQ ID NO: 82. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-334 of SEQ ID NO: 82. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 21-336 of SEQ ID NO: 82. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-334 of SEQ ID NO: 82. In some embodiments, heteromultimers of the disclosure comprise at least one ALK7 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 28-336 of SEQ ID NO: 82.

The term “Cripto-1 polypeptide” includes polypeptides comprising any naturally occurring Cripto-1 protein (encoded by TDGF1 or one of its nonhuman orthologs) as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all Cripto-1 polypeptides described herein is based on the numbering of the human Cripto-1 precursor protein sequence (SEQ ID NO: 87, NCBI Ref Seq NP_003203.1), unless specifically designated otherwise. The signal peptide is indicated by single underline. A nucleic acid sequence encoding unprocessed human Cripto-1 isoform 1 precursor protein is set forth in SEQ ID NO: 88, corresponding to nucleotides 385-948 of NCBI Reference Sequence NM_003212.3. The signal sequence is underlined. A processed Cripto-1 isoform 1 polypeptide sequence is set forth in SEQ ID NO: 89, which is encodable by a nucleic acid sequence of SEQ ID NO: 90. The human Cripto-1 isoform 2 protein sequence (NCBI Ref Seq NP_001167607.1) is set forth in SEQ ID NO: 91, which is encodable by a nucleic acid sequence of SEQ ID NO: 92, corresponding to nucleotides 43-558 of NCBI Reference Sequence NM_001174136.1. A processed Cripto-1 polypeptide sequence (isoform 2) is set forth in SEQ IDNO: 93, which is encodable by a nucleic acid sequence of SEQ ID NO: 94.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, Cripto-1 polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising a Cripto-1 polypeptide and uses thereof) are soluble (e.g., an extracellular domain of Cripto-1). In other preferred embodiments, Cripto-1 polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 87, 89, 91, or 93. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 31-82 (e.g., amino acid residues 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, or 82) of SEQ ID NO: 87, and ends at any one of amino acids 172-188 (e.g., amino acid residues 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, or 188) of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 31-188 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 63-172 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 82-172 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 82-188 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 31-172 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 63-188 of SEQ ID NO: 87. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 15-66 (e.g., amino acid residues 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, or 66) of SEQ ID NO: 91, and ends at any one of amino acids 156-172 (e.g., amino acid residues 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, or 172) of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 15-172 of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 47-172 of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 47-156 of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 66-165 of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 15-156 of SEQ ID NO: 91. In some embodiments, heteromultimers of the disclosure comprise at least one Cripto-1 polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 66-172 of SEQ ID NO: 91.

The term “Cryptic polypeptide” includes polypeptides comprising any naturally occurring Cryptic protein (encoded by CFC1 or one of its nonhuman orthologs) as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all Cryptic polypeptides described herein is based on the numbering of the human Cryptic isoform 1 precursor protein sequence (SEQ ID NO: 95, NCBI Ref Seq NP_115934.1), unless specifically designated otherwise. The signal peptide is indicated by single underline. A nucleic acid sequence encoding unprocessed human Cryptic isoform 1 precursor protein is set forth in SEQ ID NO: 96, corresponding to nucleotides 289-957 of NCBI Reference Sequence NM_032545.3. The signal sequence is underlined. A processed Cryptic isoform 1 polypeptide sequence is set forth in SEQ ID NO: 97, which is encodable by a nucleic acid sequence of SEQ ID NO: 98. The human Cryptic isoform 2 precursor protein sequence (NCBI Ref Seq NP_001257349.1) is set forth in SEQ ID NO: 99. The signal peptide is indicated by single underline. A nucleic acid sequence encoding unprocessed human Cryptic isoform 2 precursor protein is set forth in SEQ ID NO: 100, corresponding to nucleotides 289-861 of NCBI Reference Sequence NM_001270420.1. The signal sequence is underlined. A processed Cryptic isoform 2 polypeptide sequence is set forth in SEQ ID NO: 101, which is encodable by a nucleic acid sequence of SEQ ID NO: 102. The human Cryptic isoform 3 precursor protein sequence (NCBI Ref Seq NP_001257350.1) is set forth in SEQ ID NO: 103. The signal peptide is indicated by single underline. A nucleic acid sequence encoding unprocessed human Cryptic isoform 3 precursor protein is set forth in SEQ ID NO: 104, corresponding to nucleotides 289-732 of NCBI Reference Sequence NM_001270421.1. The signal sequence is underlined. A processed Cryptic isoform 3 polypeptide sequence is set forth in SEQ ID NO: 105, which is encodable by a nucleic acid sequence of SEQ IDNO: 106.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, Cryptic polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising a Cryptic polypeptide and uses thereof) are soluble (e.g., an extracellular domain of Cryptic). In other preferred embodiments, Cryptic polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 95, 97, 99, 101, 103, or 105. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 26-90 (e.g., amino acid residues 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, or 90) of SEQ ID NO: 95, and ends at any one of amino acids 157-233 (e.g., amino acid residues 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 126, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, or 233) of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-233 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-157 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 90-157 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-169 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 90-169 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 90-233 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-82 of SEQ ID NO: 95. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 26-30 (e.g., amino acid residues 26, 27, 28, 29, or 30) of SEQ ID NO: 99, and ends at any one of amino acids 82-191 (e.g., amino acid residues 82, 83, 84, 85, 86, 57, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, or 191) of SEQ ID NO: 99. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-82 of SEQ ID NO: 99. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-191 of SEQ ID NO: 99. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-82 of SEQ ID NO: 99. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-191 of SEQ ID NO: 99. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 26-30 (e.g., amino acid residues 26, 27, 28, 29, or 30) of SEQ ID NO: 103, and ends at any one of amino acids 82-148 (e.g., amino acid residues 82, 83, 84, 85, 86, 57, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, or 148) of SEQ ID NO: 103. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-148 of SEQ ID NO: 103. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-82 of SEQ ID NO: 103. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-148 of SEQ ID NO: 103. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-82 of SEQ ID NO: 103.

The term “Cryptic family protein 1B polypeptide” (Cryptic 1B) includes polypeptides comprising any naturally occurring Cryptic family protein 1B protein (encoded by CFC1B or one of its nonhuman orthologs) as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. Numbering of amino acids for all Cryptic family protein 1B polypeptides described herein is based on the numbering of the human Cryptic family protein 1B precursor protein sequence (SEQ ID NO: 107, NCBI Ref Seq NP_001072998.1, the signal peptide is indicated by single underline), unless specifically designated otherwise. A nucleic acid sequence encoding unprocessed human Cryptic family protein 1B precursor protein is set forth in SEQ ID NO: 108, corresponding to nucleotides 392-1060 of NCBI Reference Sequence NM_001079530.1. The signal sequence is underlined. A processed Cryptic family protein 1B polypeptide sequence is set forth in SEQ ID NO: 109, which is encodable by a nucleic acid sequence of SEQ ID NO: 110.

In certain embodiments, the disclosure relates to heteromultimers that comprise at least one Cryptic family protein 1B polypeptide, which includes fragments, functional variants, and modified forms thereof. Preferably, Cryptic family protein 1B polypeptides for use in accordance with inventions of the disclosure (e.g., heteromultimers comprising a Cryptic family protein 1B polypeptide and uses thereof) are soluble (e.g., an extracellular domain of Cryptic family protein 1B). In other preferred embodiments, Cryptic family protein 1B polypeptides for use in accordance with the inventions of the disclosure bind to and/or inhibit (antagonize) activity (e.g., Smad signaling) of one or more TGF-beta superfamily ligands. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of SEQ ID NOs: 107 or 109. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a polypeptide that begins at any one of amino acids of 26-30 (e.g., amino acid residues 26, 27, 28, 29, or 30) of SEQ ID NO: 107, and ends at any one of amino acids 82-223 (e.g., amino acid residues 82, 83, 84, 85, 86, 57, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 126, 217, 218, 219, 220, 221, 222, or 223) of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-223 of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-82 of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-82 of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-223 of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 26-169 of SEQ ID NO: 107. In some embodiments, heteromultimers of the disclosure comprise at least one Cryptic family protein 1B polypeptide that is at least 70%, 75%, 80%, 85%, 90%, 91%. 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to amino acids of 30-169 of SEQ ID NO: 107.

In certain aspects, the disclosure relates to homomultimers that comprise at least two ALK4 polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the ALK4 polypeptides described herein). In certain preferred embodiments, ALK4 homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two ALK5 polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the ALK5 polypeptides described herein). In certain preferred embodiments, ALK5 homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two ALK7 polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the ALK7 polypeptides described herein). In certain preferred embodiments, ALK7 homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two ActRIIA polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the ActRIIA polypeptides described herein). In certain preferred embodiments, ActRIIA homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two ActRIIB polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the ActRIIB polypeptides described herein). In certain preferred embodiments, ActRIIB homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two Cripto-1 polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the Cripto-1 polypeptides described herein). In certain preferred embodiments, Cripto-1 homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two Cryptic polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the Cryptic polypeptides described herein). In certain preferred embodiments, Cryptic homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to homomultimers that comprise at least two Cryptic 1B polypeptides, which includes fragments, functional variants, and modified forms thereof (e.g., any of the Cryptic 1B polypeptides described herein). In certain preferred embodiments, Cryptic 1B homomultimers of the disclosure are homodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK1:ActRIIB heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:ActRIIB heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK5:ActRIIB heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK7:ActRIIB heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK1:ActRIIA heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:ActRIIA heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK5:ActRIIA heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK7:ActRIIA heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:BMPRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK5:BMPRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK7:BMPRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:MISRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK5:MISRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK7:MISRII heteromultimer complexes of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK1:ALK4 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK1:ALK5 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK1:ALK7 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:ALK5 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK4:ALK7 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ALK5:ALK7 heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ActRIIA:ActRIIB heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ActRIIA:BMPRII heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ActRIIA:MISRII heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ActRIIB:BMPRII heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, ActRIIB:MISRII heteromultimers of the disclosure are heterodimers.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ALK1 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ALK4 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ALK5 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ALK7 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ALK1 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ALK4 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ALK5 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ALK7 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ALK1 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK4 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ALK4 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK5 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ALK5 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ALK7 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ALK7 heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ActRIIA heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:ActRIIB heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:BMPRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:MISRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ActRIIA heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:ActRIIB heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:BMPRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic polypeptide:MISRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIA polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ActRIIA heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one ActRIIB polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:ActRIIB heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one BMPRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:BMPRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one MISRII polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cryptic 1B:MISRII heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In some embodiments, a Cripto-1:Cryptic polypeptide heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cripto-1 polypeptide, which includes fragments, functional variants, and modified forms thereof, and at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof. In some embodiments, a Cripto-1:Cryptic 1B heteromultimer of the disclosure is a heterodimer.

In certain aspects, the disclosure relates to heteromultimers that comprise at least one Cryptic polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein), and at least one Cryptic 1B polypeptide, which includes fragments, functional variants, and modified forms thereof (e.g., any of those described herein). In certain preferred embodiments, Cryptic polypeptide:Cryptic 1B heteromultimers are soluble. In some embodiments, a Cryptic polypeptide:Cryptic 1B heteromultimer of the disclosure is a heterodimer.

In some embodiments, the present disclosure contemplates making functional variants by modifying the structure of a TGF-beta superfamily type I receptor polypeptide (e.g., ALK1, ALK4, ALK5, and ALK7), a TGF-beta superfamily type II receptor polypeptide (e.g., ActRIIA, ActRIIB, BMPRII, and MISRII), and/or a TGF-beta superfamily co-receptor (e.g., Cripto-1, Cryptic, and Cryptic 1B) for such purposes as enhancing therapeutic efficacy or stability (e.g., shelf-life and resistance to proteolytic degradation in vivo). Variants can be produced by amino acid substitution, deletion, addition, or combinations thereof. For instance, it is reasonable to expect that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (e.g., conservative mutations) will not have a major effect on the biological activity of the resulting molecule. Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Whether a change in the amino acid sequence of a polypeptide of the disclosure results in a functional homolog can be readily determined by assessing the ability of the variant polypeptide to produce a response in cells in a fashion similar to the wild-type polypeptide, or to bind to one or more TGF-beta superfamily ligands including, for example, GDF3, GDF5, GDF1, GDF8, GDF11, activin A, activin B, activin C, activin E, activin AB, activin AC, activin AE, activin BC, activin BE, Nodal.

In certain embodiments, the present disclosure contemplates specific mutations of a TGF-beta superfamily type I receptor polypeptide (e.g., ALK1, ALK2, ALK3, ALK4, ALK5, ALK6, and ALK7), a TGF-beta superfamily type II receptor polypeptide (e.g., ActRIIA, ActRIIB, BMPRII, and MISRII), and/or a TGF-beta superfamily co-receptor polypeptide (e.g., endoglin, betaglycan, Cripto-1, Cryptic, Cryptic 1B, CRIM1, CRIM2, BAMBI, BMPER, RGM-A, RGM-B, and hemojuvelin) of the disclosure so as to alter the glycosylation of the polypeptide. Such mutations may be selected so as to introduce or eliminate one or more glycosylation sites, such as O-linked or N-linked glycosylation sites. Asparagine-linked glycosylation recognition sites generally comprise a tripeptide sequence, asparagine-X-threonine or asparagine-X-serine (where “X” is any amino acid) which is specifically recognized by appropriate cellular glycosylation enzymes. The alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the polypeptide (for O-linked glycosylation sites). A variety of amino acid substitutions or deletions at one or both of the first or third amino acid positions of a glycosylation recognition site (and/or amino acid deletion at the second position) results in non-glycosylation at the modified tripeptide sequence. Another means of increasing the number of carbohydrate moieties on a polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Depending on the coupling mode used, the sugar(s) may be attached to (a) arginine and histidine; (b) free carboxyl groups; (c) free sulfhydryl groups such as those of cysteine; (d) free hydroxyl groups such as those of serine, threonine, or hydroxyproline; (e) aromatic residues such as those of phenylalanine, tyrosine, or tryptophan; or (f) the amide group of glutamine. Removal of one or more carbohydrate moieties present on a polypeptide may be accomplished chemically and/or enzymatically. Chemical deglycosylation may involve, for example, exposure of a polypeptide to the compound trifluoromethanesulfonic acid, or an equivalent compound. This treatment results in the cleavage of most or all sugars except the linking sugar (N-acetylglucosamine or N-acetylgalactosamine), while leaving the amino acid sequence intact. Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al. [Meth. Enzymol. (1987) 138:350]. The sequence of a polypeptide may be adjusted, as appropriate, depending on the type of expression system used, as mammalian, yeast, insect, and plant cells may all introduce differing glycosylation patterns that can be affected by the amino acid sequence of the peptide. In general, heteromultimers of the disclosure for use in humans may be expressed in a mammalian cell line that provides proper glycosylation, such as HEK293 or CHO cell lines, although other mammalian expression cell lines are expected to be useful as well.

The present disclosure further contemplates a method of generating mutants, particularly sets of combinatorial mutants of a TGF-beta superfamily type I receptor polypeptide (e.g., ALK1, ALK2, ALK3, ALK4, ALK5, ALK6, and ALK7), a TGF-beta superfamily type II receptor polypeptide (e.g., ActRIIA, ActRIIB, BMPRII, and MISRII), and/or TGF-beta superfamily co-receptor polypeptide (e.g., endoglin, betaglycan, Cripto-1, Cryptic, Cryptic 1B, CRIM1, CRIM2, BAMBI, BMPER, RGM-A, RGM-B, and hemojuvelin) of the present disclosure, as well as truncation mutants. Pools of combinatorial mutants are especially useful for identifying functionally active (e.g., ligand binding) TGF-beta superfamily type I receptor, TGF-beta superfamily type II receptor, and/or TGF-beta superfamily co-receptor sequences. The purpose of screening such combinatorial libraries may be to generate, for example, polypeptides variants which have altered properties, such as altered pharmacokinetic or altered ligand binding. A variety of screening assays are provided below, and such assays may be used to evaluate variants. For example, TGF-beta co-receptor variants may be screened for ability to bind to a TGF-beta superfamily ligand (e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, activin A, activin B, activin C, activin E, activin AB, activin AC, activin AE, activin BC, activin BE, nodal, glial cell-derived neurotrophic factor (GDNF), neurturin, artemin, persephin, MIS, and Lefty), to prevent binding of a TGF-beta superfamily ligand to a TGF-beta superfamily co-receptor, and/or to interfere with signaling caused by an TGF-beta superfamily ligand.

The activity of a TGF-beta superfamily receptor polypeptide, including heteromultimers and homomultimers thereof, of the disclosure also may be tested, for example in a cell-based or in vivo assay. For example, the effect of a TGF-beta superfamily receptor polypeptide on the expression of genes or the activity of proteins involved in muscle production in a muscle cell may be assessed. This may, as needed, be performed in the presence of one or more recombinant TGF-beta superfamily ligand proteins (e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, activin A, activin B, activin C, activin E, activin AB, activin AC, activin AE, activin BC, activin BE, nodal, glial cell-derived neurotrophic factor (GDNF), neurturin, artemin, persephin, MIS, and Lefty), and cells may be transfected so as to produce a TGF-beta superfamily receptor polypeptide, and optionally, a TGF-beta superfamily ligand. Likewise, a TGF-beta superfamily receptor polypeptide of the disclosure may be administered to a mouse or other animal, and one or more measurements, such as muscle formation and strength may be assessed using art-recognized methods. Similarly, the activity of a heteromultimer, or variants thereof, may be tested in osteoblasts, adipocytes, and/or neuronal cells for any effect on growth of these cells, for example, by the assays as described herein and those of common knowledge in the art. A SMAD-responsive reporter gene may be used in such cell lines to monitor effects on downstream signaling.

Combinatorial-derived variants can be generated which have increased selectivity or generally increased potency relative to a reference TGF-beta superfamily receptor polypeptide. Such variants, when expressed from recombinant DNA constructs, can be used in gene therapy protocols. Likewise, mutagenesis can give rise to variants which have intracellular half-lives dramatically different than the corresponding unmodified TGF-beta superfamily receptor polypeptide. For example, the altered protein can be rendered either more stable or less stable to proteolytic degradation or other cellular processes which result in destruction, or otherwise inactivation, of an unmodified polypeptide. Such variants, and the genes which encode them, can be utilized to alter polypeptide complex levels by modulating the half-life of the polypeptide. For instance, a short half-life can give rise to more transient biological effects and, when part of an inducible expression system, can allow tighter control of recombinant polypeptide complex levels within the cell. In an Fc fusion protein, mutations may be made in the linker (if any) and/or the Fc portion to alter one or more activities of the TGF-beta superfamily receptor polypeptide including, for example, immunogenicity, half-life, and solubility.

A combinatorial library may be produced by way of a degenerate library of genes encoding a library of polypeptides which each include at least a portion of potential TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide sequences. For instance, a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor encoding nucleotide sequences are expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display).

There are many ways by which the library of potential homologs can be generated from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be carried out in an automatic DNA synthesizer, and the synthetic genes can then be ligated into an appropriate vector for expression. The synthesis of degenerate oligonucleotides is well known in the art. See, e.g., Narang, S A (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc. 3rd Cleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam: Elsevier pp 273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477. Such techniques have been employed in the directed evolution of other proteins. See, e.g., Scott et al., (1990) Science 249:386-390; Roberts et al. (1992) PNAS USA 89:2429-2433; Devlin et al. (1990) Science 249: 404-406; Cwirla et al., (1990) PNAS USA 87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and 5,096,815.

Alternatively, other forms of mutagenesis can be utilized to generate a combinatorial library. For example, heteromultimers of the disclosure can be generated and isolated from a library by screening using, for example, alanine scanning mutagenesis [see, e.g., Ruf et al. (1994) Biochemistry 33:1565-1572; Wang et al. (1994) J. Biol. Chem. 269:3095-3099; Balint et al. (1993) Gene 137:109-118; Grodberg et al. (1993) Eur. J. Biochem. 218:597-601; Nagashima et al. (1993) J. Biol. Chem. 268:2888-2892; Lowman et al. (1991) Biochemistry 30:10832-10838; and Cunningham et al. (1989) Science 244:1081-1085], by linker scanning mutagenesis [see, e.g., Gustin et al. (1993) Virology 193:653-660; and Brown et al. (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al. (1982) Science 232:316], by saturation mutagenesis [see, e.g., Meyers et al., (1986) Science 232:613]; by PCR mutagenesis [see, e.g., Leung et al. (1989) Method Cell Mol Biol 1:11-19]; or by random mutagenesis, including chemical mutagenesis [see, e.g., Miller et al. (1992) A Short Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor, N.Y.; and Greener et al. (1994) Strategies in Mol Biol 7:32-34]. Linker scanning mutagenesis, particularly in a combinatorial setting, is an attractive method for identifying truncated (bioactive) forms of TGF-beta superfamily type I receptor, type II receptor, and/or co-receptor polypeptides.

A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations and truncations, and, for that matter, for screening cDNA libraries for gene products having a certain property. Such techniques will be generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of heteromultimers of the disclosure. The most widely used techniques for screening large gene libraries typically comprise cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Preferred assays include TGF-beta superfamily ligand (e.g., BMP2, BMP2/7, BMP3, BMP4, BMP4/7, BMP5, BMP6, BMP7, BMP8a, BMP8b, BMP9, BMP10, GDF3, GDF5, GDF6/BMP13, GDF7, GDF8, GDF9b/BMP15, GDF11/BMP11, GDF15/MIC1, activin A, activin B, activin C, activin E, activin AB, activin AC, activin AE, activin BC, activin BE, nodal, glial cell-derived neurotrophic factor (GDNF), neurturin, artemin, persephin, MIS, and Lefty) binding assays and/or TGF-beta superfamily ligand-mediated cell signaling assays.

In certain embodiments, heteromultimers TGF-beta superfamily receptor polypeptide, including heteromultimers and homomultimers thereof) of the disclosure may further comprise post-translational modifications in addition to any that are naturally present in the TGF-beta superfamily type I receptor, type II receptor, or co-receptor polypeptide. Such modifications include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. As a result, the TGF-beta superfamily receptor polypeptide may comprise non-amino acid elements, such as polyethylene glycols, lipids, polysaccharide or monosaccharide, and phosphates. Effects of such non-amino acid elements on the functionality of a TGF-beta superfamily receptor polypeptide may be tested as described herein for other TGF-beta superfamily receptor polypeptide variants. When a polypeptide of the disclosure is produced in cells by cleaving a nascent form of the polypeptide, post-translational processing may also be important for correct folding and/or function of the protein. Different cells (e.g., CHO, HeLa, MDCK, 293, WI38, NIH-3T3 or HEK293) have specific cellular machinery and characteristic mechanisms for such post-translational activities and may be chosen to ensure the correct modification and processing of the TGF-beta superfamily type I receptor, type II receptor, and/or co-receptor polypeptides as well as heteromultimers comprising the same.

In some embodiments, TGF-beta superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides further comprise one or more heterologous portions (e.g., a polypeptide comprising a TGF-beta superfamily type I receptor polypeptide domain and second polypeptide domain that is heterologous to the TGF-beta superfamily type I receptor polypeptide domain) so as to confer a desired property. For example, some fusion domains are particularly useful for isolation of the fusion proteins by affinity chromatography. Well-known examples of such fusion domains include, but are not limited to, polyhistidine, Glu-Glu, glutathione S-transferase (GST), thioredoxin, protein A, protein G, an immunoglobulin heavy-chain constant region (Fc), maltose binding protein (MBP), or human serum albumin. For the purpose of affinity purification, relevant matrices for affinity chromatography, such as glutathione-, amylase-, and nickel- or cobalt-conjugated resins are used. Many of such matrices are available in “kit” form, such as the Pharmacia GST purification system and the QIAexpress™ system (Qiagen) useful with (HIS₆) (SEQ ID NO: 225) fusion partners. As another example, a fusion domain may be selected so as to facilitate detection of the polypeptides. Examples of such detection domains include the various fluorescent proteins (e.g., GFP) as well as “epitope tags,” which are usually short peptide sequences for which a specific antibody is available. Well-known epitope tags for which specific monoclonal antibodies are readily available include FLAG, influenza virus haemagglutinin (HA), and c-myc tags. In some cases, the fusion domains have a protease cleavage site, such as for factor Xa or thrombin, which allows the relevant protease to partially digest the fusion proteins and thereby liberate the recombinant proteins therefrom. The liberated proteins can then be isolated from the fusion domain by subsequent chromatographic separation.

In some embodiments, TGF-beta superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides of the present disclosure comprise one or more modifications that are capable of stabilizing the polypeptides. For example, such modifications enhance the in vitro half-life of the polypeptides, enhance circulatory half-life of the polypeptides, and/or reduce proteolytic degradation of the polypeptides. Such stabilizing modifications include, but are not limited to, fusion proteins (including, for example, fusion proteins comprising a type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide domain and a stabilizer domain), modifications of a glycosylation site (including, for example, addition of a glycosylation site to a polypeptide of the disclosure), and modifications of carbohydrate moiety (including, for example, removal of carbohydrate moieties from a polypeptide of the disclosure). As used herein, the term “stabilizer domain” not only refers to a fusion domain (e.g., an immunoglobulin Fc domain) as in the case of fusion proteins, but also includes nonproteinaceous modifications such as a carbohydrate moiety, or nonproteinaceous moiety, such as polyethylene glycol.

It is understood that different elements of a fusion protein (e.g., immunoglobulin Fc fusion protein) may be arranged in any manner that is consistent with desired functionality. For example, a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide domain may be placed C-terminal to a heterologous domain, or alternatively, a heterologous domain may be placed C-terminal to a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide domain. The TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor domain and the heterologous domain need not be adjacent in a fusion protein, and additional domains or amino acid sequences may be included C- or N-terminal to either domain or between the domains.

For example, a TGF-beta superfamily type I receptor, type II receptor, or co-receptor fusion protein may comprise an amino acid sequence as set forth in the formula A-B-C. The B portion corresponds to a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide domain. The A and C portions may be independently zero, one, or more than one amino acid, and both the A and C portions when present are heterologous to B. The A and/or C portions may be attached to the B portion via a linker sequence. A linker may be rich in glycine (e.g., 2-10, 2-5, 2-4, 2-3 glycine residues) or glycine and proline residues and may, for example, contain a single sequence of threonine/serine and glycines or repeating sequences of threonine/serine and/or glycines (e.g., GGG (SEQ ID NO: 223), GGGG (SEQ ID NO: 222), TGGGG (SEQ ID NO: 219), SGGGG (SEQ ID NO: 220), TGGG (SEQ ID NO: 217), GGGS (SEQ ID NO: 221224), or SGGG (SEQ ID NO: 218)), singlets, or repeats. In certain embodiments, a TGF-beta superfamily type I receptor, type II receptor, or co-receptor fusion protein comprises an amino acid sequence as set forth in the formula A-B-C, wherein A is a leader (signal) sequence, B consists of a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide domain, and C is a polypeptide portion that enhances one or more of in vivo stability, in vivo half-life, uptake/administration, tissue localization or distribution, formation of protein complexes, and/or purification. In certain embodiments, a TGF-beta superfamily type I receptor, type II receptor, or co-receptor fusion protein comprises an amino acid sequence as set forth in the formula A-B-C, wherein A is a TPA leader sequence, B consists of a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide domain, and C is an immunoglobulin Fc domain.

As specific examples, the present disclosure provides fusion proteins comprising TGF-beta superfamily type I receptor, type II receptor, or co-receptor polypeptides fused to a polypeptide comprising a constant domain of an immunoglobulin, such as a CH1, CH2, or CH3 domain of an immunoglobulin or an Fc domain. Fc domains derived from human IgG1, IgG2, IgG3, and IgG4 are provided herein. Other mutations are known that decrease either CDC or ADCC activity, and collectively, any of these variants are included in the disclosure and may be used as advantageous components of a heteromultimers of the disclosure. Optionally, the IgG1 Fc domain of SEQ ID NO: 135 has one or more mutations at residues such as Asp-265, Lys-322, and Asn-434 (numbered in accordance with the corresponding full-length IgG1). In certain cases, the mutant Fc domain having one or more of these mutations (e.g., Asp-265 mutation) has reduced ability of binding to the Fcγ receptor relative to a wildtype Fc domain. In other cases, the mutant Fc domain having one or more of these mutations (e.g., Asn-434 mutation) has increased ability of binding to the MHC class I-related Fc-receptor (FcRN) relative to a wildtype Fc domain.

An example of a native amino acid sequence that may be used for the Fc portion of human IgG1 (G1Fc) is shown below (SEQ ID NO: 135). Dotted underline indicates the hinge region, and solid underline indicates positions with naturally occurring variants. In part, the disclosure provides polypeptides comprising an amino acid sequence with 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 135. Naturally occurring variants in G1Fc would include E134D and M136L according to the numbering system used in SEQ ID NO: 135 (see Uniprot P01857).

An example of a native amino acid sequence that may be used for the Fc portion of human IgG2 (G2Fc) is shown below (SEQ ID NO: 136). Dotted underline indicates the hinge region and double underline indicates positions where there are data base conflicts in the sequence (according to UniProt P01859). In part, the disclosure provides polypeptides comprising an amino acid sequence with 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 136.

Two examples of amino acid sequences that may be used for the Fc portion of human IgG3 (G3Fc) are shown below. The hinge region in G3Fc can be up to four times as long as in other Fc chains and contains three identical 15-residue segments preceded by a similar 17-residue segment. The first G3Fc sequence shown below (SEQ ID NO: 137) contains a short hinge region consisting of a single 15-residue segment, whereas the second G3Fc sequence (SEQ ID NO: 138) contains a full-length hinge region. In each case, dotted underline indicates the hinge region, and solid underline indicates positions with naturally occurring variants according to UniProt P01859. In part, the disclosure provides polypeptides comprising an amino acid sequence with 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 137 or 138.

Naturally occurring variants in G3Fc (for example, see Uniprot P01860) include E68Q, P76L, E79Q, Y81F, D97N, N100D, T124A, S169N, S169del, F221Y when converted to the numbering system used in SEQ ID NO: 137, and the present disclosure provides fusion proteins comprising G3Fc domains containing one or more of these variations. In addition, the human immunoglobulin IgG3 gene (IGHG3) shows a structural polymorphism characterized by different hinge lengths (see Uniprot P01859). Specifically, variant WIS is lacking most of the V region and all of the CH1 region. It has an extra interchain disulfide bond at position 7 in addition to the 11 normally present in the hinge region. Variant ZUC lacks most of the V region, all of the CH1 region, and part of the hinge. Variant OMM may represent an allelic form or another gamma chain subclass. The present disclosure provides additional fusion proteins comprising G3Fc domains containing one or more of these variants.

An example of a native amino acid sequence that may be used for the Fc portion of human IgG4 (G4Fc) is shown below (SEQ ID NO: 139). Dotted underline indicates the hinge region. In part, the disclosure provides polypeptides comprising an amino acid sequence with 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to SEQ ID NO: 139.

A variety of engineered mutations in the Fc domain are presented herein with respect to the G1Fc sequence (SEQ ID NO: 135), and analogous mutations in G2Fc, G3Fc, and G4Fc can be derived from their alignment with G1Fc in FIG. 4. Due to unequal hinge lengths, analogous Fc positions based on isotype alignment (FIG. 4) possess different amino acid numbers in SEQ ID NOs: 135, 136, 137, and 139. It can also be appreciated that a given amino acid position in an immunoglobulin sequence consisting of hinge, C_(H)2, and C_(H)3 regions (e.g., SEQ ID NOs: 135, 136, 137, 138, or 139) will be identified by a different number than the same position when numbering encompasses the entire IgG1 heavy-chain constant domain (consisting of the C_(H)1, hinge, C_(H)2, and C_(H)3 regions) as in the Uniprot database. For example, correspondence between selected C_(H)3 positions in a human G1Fc sequence (SEQ ID NO: 135), the human IgG1 heavy chain constant domain (Uniprot P01857), and the human IgG1 heavy chain is as follows.

TABLE 1 Correspondence of C_(H)3 Positions in Different Numbering Systems G1Fc IgG1 heavy chain IgG1 heavy chain (Numbering begins constant domain (EU numbering scheme at first threonine (Numbering begins of Kabat et al., in hinge region) at C_(H)1) 1991*) Y127 Y232 Y349 S132 S237 S354 E134 E239 E356 T144 T249 T366 L146 L251 L368 K170 K275 K392 D177 D282 D399 Y185 Y290 Y407 K187 K292 K409 *Kabat et al. (eds) 1991; pp. 688-696 in Sequences of Proteins of Immunological Interest, 5^(th) ed., Vol. 1, NIH, Bethesda, MD.

In certain aspects, a TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide (e.g., those described herein) may form heteromultimers, covalently or non-covalently, with at least one additional TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide. Many methods known in the art can be used to generate heteromultimers. For example, non-naturally occurring disulfide bonds may be constructed by replacing on a first polypeptide (e.g., TGF-beta superfamily type I polypeptide) a naturally occurring amino acid with a free thiol-containing residue, such as cysteine, such that the free thiol interacts with another free thiol-containing residue on a second polypeptide (e.g., TGF-beta superfamily type II polypeptide) such that a disulfide bond is formed between the first and second polypeptides. Additional examples of interactions to promote heteromultimer formation include, but are not limited to, ionic interactions such as described in Kjaergaard et al., WO2007147901; electrostatic steering effects such as described in Kannan et al., U.S. Pat. No. 8,592,562; coiled-coil interactions such as described in Christensen et al., U.S.20120302737; leucine zippers such as described in Pack & Plueckthun, (1992) Biochemistry 31: 1579-1584; and helix-turn-helix motifs such as described in Pack et al., (1993) Bio/Technology 11: 1271-1277. Linkage of the various segments may be obtained via, e.g., covalent binding such as by chemical cross-linking, peptide linkers, disulfide bridges, etc., or affinity interactions such as by avidin-biotin or leucine zipper technology. Preferably, polypeptides disclosed herein form heterodimers, although higher order heteromultimers are also included such as, but not limited to, heterotrimers, heterotetramers, and further oligomeric structures (see, e.g., FIGS. 5 and 6).

In some embodiments, TGF-beta superfamily type I receptor, type II receptor, and/or co-receptor polypeptides of the present disclosure comprise at least one multimerization domain. As disclosed herein, the term “multimerization domain” refers to an amino acid or sequence of amino acids that promote covalent or non-covalent interaction between at least a first polypeptide and at least a second polypeptide. Polypeptides disclosed herein may be joined covalently or non-covalently to a multimerization domain. In some embodiments, a multimerization domain promotes interaction between a first polypeptide and a second polypeptide to promote heteromultimer formation (e.g., heterodimer formation), and optionally hinders or otherwise disfavors homomultimer formation (e.g., homodimer formation), thereby increasing the yield of desired heteromultimer (see, e.g., FIGS. 5 and 6).

In certain aspects, a multimerization domain may comprise one component of an interaction pair. In some embodiments, the polypeptides disclosed herein may form protein complexes comprising a first polypeptide covalently or non-covalently associated with a second polypeptide, wherein the first polypeptide comprises the amino acid sequence of a first TGF-beta superfamily receptor polypeptide and the amino acid sequence of a first member of an interaction pair; and the second polypeptide comprises the amino acid sequence of a second TGF-beta superfamily receptor polypeptide and the amino acid sequence of a second member of an interaction pair. The interaction pair may be any two polypeptide sequences that interact to form a complex, particularly a heterodimeric complex although operative embodiments may also employ an interaction pair that can form a homodimeric complex. An interaction pair may be selected to confer an improved property/activity such as increased serum half-life, or to act as an adaptor on to which another moiety is attached to provide an improved property/activity. For example, a polyethylene glycol moiety may be attached to one or both components of an interaction pair to provide an improved property/activity such as improved serum half-life.

The first and second members of the interaction pair may be an asymmetric pair, meaning that the members of the pair preferentially associate with each other rather than self-associate. Accordingly, first and second members of an asymmetric interaction pair may associate to form, or example, a heterodimeric complex (see, e.g., FIGS. 5A and 5B). Alternatively, the interaction pair may be unguided, meaning that the members of the pair may associate with each other or self-associate without substantial preference and thus may have the same or different amino acid sequences. Accordingly, first and second members of an unguided interaction pair may associate to form a homodimer complex or a heterodimeric complex. Optionally, the first member of the interaction pair (e.g., an asymmetric pair or an unguided interaction pair) associates covalently with the second member of the interaction pair. Optionally, the first member of the interaction pair (e.g., an asymmetric pair or an unguided interaction pair) associates non-covalently with the second member of the interaction pair.

A problem that arises in large-scale production of asymmetric immunoglobulin-based proteins from a single cell line is known as the “chain association issue”. As confronted prominently in the production of bispecific antibodies, the chain-association issue concerns the challenge of efficiently producing a desired multichain protein from among the multiple combinations that inherently result when different heavy chains and/or light chains are produced in a single cell line (see, for example, Klein et al (2012) mAbs 4:653-663). This problem is most acute when two different heavy chains and two different light chains are produced in the same cell, in which case there are a total of 16 possible chain combinations (although some of these are identical) when only one is typically desired. Nevertheless, the same principle accounts for diminished yield of a desired multichain fusion protein that incorporates only two different (asymmetric) heavy chains.

Various methods are known in the art that increase desired pairing of Fc-containing fusion polypeptide chains in a single cell line to produce a preferred asymmetric fusion protein at acceptable yields (see, for example, Klein et al (2012) mAbs 4:653-663; and Spiess et al (2015) Molecular Immunology 67(2A): 95-106). Methods to obtain desired pairing of Fc-containing chains include, but are not limited to, charge-based pairing (electrostatic steering), “knobs-into-holes” steric pairing, SEEDbody pairing, and leucine zipper-based pairing. See, for example, Ridgway et al (1996) Protein Eng 9:617-621; Merchant et al (1998) Nat Biotech 16:677-681; Davis et al (2010) Protein Eng Des Sel 23:195-202; Gunasekaran et al (2010); 285:19637-19646; Wranik et al (2012) J Biol Chem 287:43331-43339; U.S. Pat. No. 5,932,448; WO 1993/011162; WO 2009/089004, and WO 2011/034605. As described herein, these methods may be used to generate heterodimers comprising two or more TGF-beta superfamily receptor polypeptides. See FIGS. 5 and 6.

For example, one means by which interaction between specific polypeptides may be promoted is by engineering protuberance-into-cavity (knob-into-holes) complementary regions such as described in Arathoon et al., U.S. Pat. No. 7,183,076 and Carter et al., U.S. Pat. No. 5,731,168. “Protuberances” are constructed by replacing small amino acid side chains from the interface of the first polypeptide (e.g., a first interaction pair) with larger side chains (e.g., tyrosine or tryptophan). Complementary “cavities” of identical or similar size to the protuberances are optionally created on the interface of the second polypeptide (e.g., a second interaction pair) by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). Where a suitably positioned and dimensioned protuberance or cavity exists at the interface of either the first or second polypeptide, it is only necessary to engineer a corresponding cavity or protuberance, respectively, at the adjacent interface.

At neutral pH (7.0), aspartic acid and glutamic acid are negatively charged and lysine, arginine, and histidine are positively charged. These charged residues can be used to promote heterodimer formation and at the same time hinder homodimer formation. Attractive interactions take place between opposite charges and repulsive interactions occur between like charges. In part, protein complexes disclosed herein make use of the attractive interactions for promoting heteromultimer formation (e.g., heterodimer formation), and optionally repulsive interactions for hindering homodimer formation (e.g., homodimer formation) by carrying out site directed mutagenesis of charged interface residues.

For example, the IgG1 CH3 domain interface comprises four unique charge residue pairs involved in domain-domain interactions: Asp356-Lys439′, Glu357-Lys370′, Lys392-Asp399′, and Asp399-Lys409′ (residue numbering in the second chain is indicated by (′)). It should be noted that the numbering scheme used here to designate residues in the IgG1 CH3 domain conforms to the EU numbering scheme of Kabat. Due to the 2-fold symmetry present in the CH3-CH3 domain interactions, each unique interaction will represented twice in the structure (e.g., Asp-399-Lys409′ and Lys409-Asp399′). In the wild-type sequence, K409-D399′ favors both heterodimer and homodimer formation. A single mutation switching the charge polarity (e.g., K409E; positive to negative charge) in the first chain leads to unfavorable interactions for the formation of the first chain homodimer. The unfavorable interactions arise due to the repulsive interactions occurring between the same charges (negative-negative; K409E-D399′ and D399-K409E′). A similar mutation switching the charge polarity (D399K′; negative to positive) in the second chain leads to unfavorable interactions (K409′-D399K′ and D399K-K409′) for the second chain homodimer formation. But, at the same time, these two mutations (K409E and D399K′) lead to favorable interactions (K409E-D399K′ and D399-K409′) for the heterodimer formation.

The electrostatic steering effect on heterodimer formation and homodimer discouragement can be further enhanced by mutation of additional charge residues which may or may not be paired with an oppositely charged residue in the second chain including, for example, Arg355 and Lys360. The Table 2 below lists possible charge change mutations that can be used, alone or in combination, to enhance heteromultimer formation of the heteromultimers disclosed herein.

TABLE 2 Examples of Pair-Wise Charged Residue Mutations to Enhance Heterodimer Formation Interacting Corresponding Position in Mutation in position in mutation in first chain first chain second chain second chain Lys409 Asp or Glu Asp399′ Lys, Arg, or His Lys392 Asp or Glu Asp399′ Lys, Arg, or His Lys439 Asp or Glu Asp356′ Lys, Arg, or His Lys370 Asp or Glu Glu357′ Lys, Arg, or His Asp399 Lys, Arg, or His Lys409′ Asp or Glu Asp399 Lys, Arg, or His Lys392′ Asp or Glu Asp356 Lys, Arg, or His Lys439′ Asp or Glu Glu357 Lys, Arg, or His Lys370′ Asp or Glu

In some embodiments, one or more residues that make up the CH3-CH3 interface in a fusion protein of the instant application are replaced with a charged amino acid such that the interaction becomes electrostatically unfavorable. For example, a positively-charged amino acid in the interface (e.g., a lysine, arginine, or histidine) is replaced with a negatively charged amino acid (e.g., aspartic acid or glutamic acid). Alternatively, or in combination with the forgoing substitution, a negatively-charged amino acid in the interface is replaced with a positively-charged amino acid. In certain embodiments, the amino acid is replaced with a non-naturally occurring amino acid having the desired charge characteristic. It should be noted that mutating negatively charged residues (Asp or Glu) to His will lead to increase in side chain volume, which may cause steric issues. Furthermore, His proton donor- and acceptor-form depends on the localized environment. These issues should be taken into consideration with the design strategy. Because the interface residues are highly conserved in human and mouse IgG subclasses, electrostatic steering effects disclosed herein can be applied to human and mouse IgG1, IgG2, IgG3, and IgG4. This strategy can also be extended to modifying uncharged residues to charged residues at the CH3 domain interface.

In part, the disclosure provides desired pairing of asymmetric Fc-containing polypeptide chains using Fc sequences engineered to be complementary on the basis of charge pairing (electrostatic steering). One of a pair of Fc sequences with electrostatic complementarity can be arbitrarily fused to the TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide of the construct, with or without an optional linker, to generate a TGF-beta superfamily type I, type II, or co-receptor receptor fusion polypeptide. This single chain can be coexpressed in a cell of choice along with the Fc sequence complementary to the first Fc to favor generation of the desired multichain construct (e.g., a TGF-beta superfamily heteromultimer). In this example based on electrostatic steering, SEQ ID NO: 140 (human G1Fc(E134K/D177K)) and SEQ ID NO: 141 (human G1Fc(K170D/K187D)) are examples of complementary Fc sequences in which the engineered amino acid substitutions are double underlined, and the TGF-beta superfamily type I, type II receptor, or co-receptor polypeptide of the construct can be fused to either SEQ ID NO: 140 or SEQ ID NO: 141, but not both. Given the high degree of amino acid sequence identity between native hG1Fc, native hG2Fc, native hG3Fc, and native hG4Fc, it can be appreciated that amino acid substitutions at corresponding positions in hG2Fc, hG3Fc, or hG4Fc (see FIG. 4) will generate complementary Fc pairs which may be used instead of the complementary hG1Fc pair below (SEQ ID NOs: 140 and 141).

In part, the disclosure provides desired pairing of asymmetric Fc-containing polypeptide chains using Fc sequences engineered for steric complementarity. In part, the disclosure provides knobs-into-holes pairing as an example of steric complementarity. One of a pair of Fc sequences with steric complementarity can be arbitrarily fused to the TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide of the construct, with or without an optional linker, to generate a TGF-beta superfamily type I, type II, or co-receptor fusion polypeptide. This single chain can be coexpressed in a cell of choice along with the Fc sequence complementary to the first Fc to favor generation of the desired multichain construct. In this example based on knobs-into-holes pairing, SEQ ID NO: 142 (human G1Fc(T144Y)) and SEQ ID NO: 143 (human G1Fc(Y185T)) are examples of complementary Fc sequences in which the engineered amino acid substitutions are double underlined, and the TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide of the construct can be fused to either SEQ ID NO: 142 or SEQ ID NO: 143, but not both. Given the high degree of amino acid sequence identity between native hG1Fc, native hG2Fc, native hG3Fc, and native hG4Fc, it can be appreciated that amino acid substitutions at corresponding positions in hG2Fc, hG3Fc, or hG4Fc (see FIG. 4) will generate complementary Fc pairs which may be used instead of the complementary hG1Fc pair below (SEQ ID NOs: 142 and 143).

An example of Fc complementarity based on knobs-into-holes pairing combined with an engineered disulfide bond is disclosed in SEQ ID NO: 144 (hG1Fc(S132C/T144W)) and SEQ ID NO: 145 (hG1Fc(Y127C/T144S/L146A/Y185V)). The engineered amino acid substitutions in these sequences are double underlined, and the TGF-beta superfamily type I, type II or co-receptor of the construct can be fused to either SEQ ID NO: 144 or SEQ ID NO: 145, but not both. Given the high degree of amino acid sequence identity between native hG1Fc, native hG2Fc, native hG3Fc, and native hG4Fc, it can be appreciated that amino acid substitutions at corresponding positions in hG2Fc, hG3Fc, or hG4Fc (see FIG. 4) will generate complementary Fc pairs which may be used instead of the complementary hG1Fc pair below (SEQ ID NOs: 144 and 145).

In part, the disclosure provides desired pairing of asymmetric Fc-containing polypeptide chains using Fc sequences engineered to generate interdigitating β-strand segments of human IgG and IgA C_(H)3 domains. Such methods include the use of strand-exchange engineered domain (SEED) C_(H)3 heterodimers allowing the formation of SEEDbody fusion proteins (see, for example, Davis et al (2010) Protein Eng Design Sel 23:195-202). One of a pair of Fc sequences with SEEDbody complementarity can be arbitrarily fused to the TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide or co-receptor polypeptide of the construct, with or without an optional linker, to generate a TGF-beta superfamily fusion polypeptide. This single chain can be coexpressed in a cell of choice along with the Fc sequence complementary to the first Fc to favor generation of the desired multichain construct. In this example based on SEEDbody (Sb) pairing, SEQ ID NO: 146 (hG1Fc(Sb_(AG))) and SEQ ID NO: 147 (hG1Fc(Sb_(GA))) are examples of complementary IgG Fc sequences in which the engineered amino acid substitutions from IgA Fc are double underlined, and the TGF-beta superfamily type I, type II, or co-receptor polypeptide of the construct can be fused to either SEQ ID NO: 146 or SEQ ID NO: 147, but not both. Given the high degree of amino acid sequence identity between native hG1Fc, native hG2Fc, native hG3Fc, and native hG4Fc, it can be appreciated that amino acid substitutions at corresponding positions in hG1Fc, hG2Fc, hG3Fc, or hG4Fc (see FIG. 4) will generate an Fc monomer which may be used in the complementary IgG-IgA pair below (SEQ ID NOs: 146 and 147).

In part, the disclosure provides desired pairing of asymmetric Fc-containing polypeptide chains with a cleavable leucine zipper domain attached at the C-terminus of the Fc C_(H)3 domains. Attachment of a leucine zipper is sufficient to cause preferential assembly of heterodimeric antibody heavy chains. See, e.g., Wranik et al (2012) J Biol Chem 287:43331-43339. As disclosed herein, one of a pair of Fc sequences attached to a leucine zipper-forming strand can be arbitrarily fused to the TGF-beta superfamily type I receptor polypeptide, type II receptor polypeptide, or co-receptor polypeptide of the construct, with or without an optional linker, to generate a TGF-beta superfamily fusion polypeptide. This single chain can be coexpressed in a cell of choice along with the Fc sequence attached to a complementary leucine zipper-forming strand to favor generation of the desired multichain construct. Proteolytic digestion of the construct with the bacterial endoproteinase Lys-C post purification can release the leucine zipper domain, resulting in an Fc construct whose structure is identical to that of native Fc. In this example based on leucine zipper pairing, SEQ ID NO: 148 (hG1Fc-Ap1 (acidic)) and SEQ ID NO: 149 (hG1Fc-Bp1 (basic)) are examples of complementary IgG Fc sequences in which the engineered complimentary leucine zipper sequences are underlined, and the TGF-beta superfamily type I, type II, or co-receptor polypeptide or co-receptor polypeptide of the construct can be fused to either SEQ ID NO: 148 or SEQ ID NO: 149, but not both. Given the high degree of amino acid sequence identity between native hG1Fc, native hG2Fc, native hG3Fc, and native hG4Fc, it can be appreciated that leucine zipper-forming sequences attached, with or without an optional linker, to hG1Fc, hG2Fc, hG3Fc, or hG4Fc (see FIG. 4) will generate an Fc monomer which may be used in the complementary leucine zipper-forming pair below (SEQ ID NOs: 148 and 149).

In preferred embodiments, TGF-beta superfamily receptor polypeptides, including heteromultimers and homomultimers thereof, to be used in accordance with the methods described herein are isolated polypeptide complexes. As used herein, an isolated protein (or protein complex) or polypeptide (or polypeptide complex) is one which has been separated from a component of its natural environment. In some embodiments, a heteromultimer complex of the disclosure is purified to greater than 95%, 96%, 97%, 98%, or 99% purity as determined by, for example, electrophoretic (e.g., SDS-PAGE, isoelectric focusing (IEF), capillary electrophoresis) or chromatographic (e.g., ion exchange or reverse phase HPLC). Methods for assessment of antibody purity are well known in the art (See, e.g., Flatman et al., (2007) J. Chromatogr. B 848:79-87). In some embodiments, heteromultimer preparations of the disclosure are substantially free of TGF-beta superfamily type I receptor polypeptide homomultimers, TGF-beta superfamily type II receptor polypeptide homomultimers, and/or TGF-beta superfamily co-receptor polypeptide homomultimers. For example, in some embodiments, heteromultimer preparations comprise less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily type I receptor polypeptide homomultimers. In some embodiments, heteromultimer preparations comprise less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily type II receptor polypeptide homomultimers. In some embodiments, heteromultimer preparations comprise less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily co-receptor polypeptide homomultimers. In some embodiments, heteromultimer preparations comprise less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily type I receptor polypeptide homomultimers and less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily co-receptor polypeptide homomultimers. In some embodiments, heteromultimer preparations comprise less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily type II receptor polypeptide homomultimers and less than about 10%, 9%, 8%, 7%, 5%, 4%, 3%, 2%, or less than 1% of TGF-beta superfamily co-receptor polypeptide homomultimers.

In certain embodiments, TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and co-receptor polypeptides as well as heteromultimer complexes thereof, of the disclosure can be produced by a variety of art-known techniques. For example, polypeptides of the disclosure can be synthesized using standard protein chemistry techniques such as those described in Bodansky, M. Principles of Peptide Synthesis, Springer Verlag, Berlin (1993) and Grant G. A. (ed.), Synthetic Peptides: A User's Guide, W. H. Freeman and Company, New York (1992). In addition, automated peptide synthesizers are commercially available (see, e.g., Advanced ChemTech Model 396; Milligen/Biosearch 9600). Alternatively, the polypeptides and complexes of the disclosure, including fragments or variants thereof, may be recombinantly produced using various expression systems (e.g., E. coli, Chinese Hamster Ovary (CHO) cells, COS cells, baculovirus) as is well known in the art. In a further embodiment, the modified or unmodified polypeptides of the disclosure may be produced by digestion of recombinantly produced full-length TGFβ superfamily type I receptor, type II receptor and/or co-receptor polypeptides by using, for example, a protease, e.g., trypsin, thermolysin, chymotrypsin, pepsin, or paired basic amino acid converting enzyme (PACE). Computer analysis (using commercially available software, e.g., MacVector, Omega, PCGene, Molecular Simulation, Inc.) can be used to identify proteolytic cleavage sites.

3. Nucleic Acids Encoding TGFβ Superfamily Type I Receptor Polypeptides, Type II Receptor Polypeptides, and Co-Receptor Polypeptides

In certain embodiments, the present disclosure provides isolated and/or recombinant nucleic acids encoding TGFβ superfamily type I receptors, type II receptors, and co-receptors (including fragments, functional variants, and fusion proteins thereof) disclosed herein. For example, SEQ ID NO: 13 encodes a naturally occurring human ActRIIA precursor polypeptide, while SEQ ID NO: 14 encodes a processed extracellular domain of ActRIIA. The subject nucleic acids may be single-stranded or double stranded. Such nucleic acids may be DNA or RNA molecules. These nucleic acids may be used, for example, in methods for making TGF-beta superfamily heteromultimers of the present disclosure.

As used herein, isolated nucleic acid(s) refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that ordinarily contain the nucleic acid molecule, but the nucleic acid molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.

In certain embodiments, nucleic acids encoding TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides of the present disclosure are understood to include nucleic acids of any one of SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210, as well as variants thereof. Variant nucleotide sequences include sequences that differ by one or more nucleotide substitutions, additions, or deletions including allelic variants, and therefore, will include coding sequences that differ from the nucleotide sequence designated in any one of SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210.

In certain embodiments, TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides of the present disclosure are encoded by isolated or recombinant nucleic acid sequences that are at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210. One of ordinary skill in the art will appreciate that nucleic acid sequences that are at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequences complementary to SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210 are also within the scope of the present disclosure. In further embodiments, the nucleic acid sequences of the disclosure can be isolated, recombinant, and/or fused with a heterologous nucleotide sequence or in a DNA library.

In other embodiments, nucleic acids of the present disclosure also include nucleotide sequences that hybridize under highly stringent conditions to the nucleotide sequence designated in SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210, the complement sequence of SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210, or fragments thereof. One of ordinary skill in the art will understand readily that appropriate stringency conditions which promote DNA hybridization can be varied. For example, one could perform the hybridization at 6.0×sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2.0×SSC at 50° C. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0×SSC at 50° C. to a high stringency of about 0.2×SSC at 50° C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22° C., to high stringency conditions at about 65° C. Both temperature and salt may be varied, or temperature or salt concentration may be held constant while the other variable is changed. In one embodiment, the disclosure provides nucleic acids which hybridize under low stringency conditions of 6×SSC at room temperature followed by a wash at 2×SSC at room temperature.

Isolated nucleic acids which differ from the nucleic acids as set forth in SEQ ID NOs: 7, 8, 13, 14, 35, 37, 39, 41, 43, 45, 47, 49, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 179, 183, 185, 186, 191, 194, 195, 200, 203, and 210due to degeneracy in the genetic code are also within the scope of the disclosure. For example, a number of amino acids are designated by more than one triplet. Codons that specify the same amino acid, or synonyms (for example, CAU and CAC are synonyms for histidine) may result in “silent” mutations which do not affect the amino acid sequence of the protein. However, it is expected that DNA sequence polymorphisms that do lead to changes in the amino acid sequences of the subject proteins will exist among mammalian cells. One skilled in the art will appreciate that these variations in one or more nucleotides (up to about 3-5% of the nucleotides) of the nucleic acids encoding a particular protein may exist among individuals of a given species due to natural allelic variation. Any and all such nucleotide variations and resulting amino acid polymorphisms are within the scope of this disclosure.

In certain embodiments, the recombinant nucleic acids of the present disclosure may be operably linked to one or more regulatory nucleotide sequences in an expression construct. Regulatory nucleotide sequences will generally be appropriate to the host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells. Typically, said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, and enhancer or activator sequences. Constitutive or inducible promoters as known in the art are contemplated by the disclosure. The promoters may be either naturally occurring promoters, or hybrid promoters that combine elements of more than one promoter. An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome. In some embodiments, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selectable marker genes are well known in the art and will vary with the host cell used.

In certain aspects of the present disclosure, the subject nucleic acid is provided in an expression vector comprising a nucleotide sequence encoding a TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide and operably linked to at least one regulatory sequence. Regulatory sequences are art-recognized and are selected to direct expression of the TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide. Accordingly, the term regulatory sequence includes promoters, enhancers, and other expression control elements. Exemplary regulatory sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology, Academic Press, San Diego, Calif. (1990). For instance, any of a wide variety of expression control sequences that control the expression of a DNA sequence when operatively linked to it may be used in these vectors to express DNA sequences encoding a TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide. Such useful expression control sequences, include, for example, the early and late promoters of SV40, tet promoter, adenovirus or cytomegalovirus immediate early promoter, RSV promoters, the lac system, the trp system, the TAC or TRC system, T7 promoter whose expression is directed by T7 RNA polymerase, the major operator and promoter regions of phage lambda, the control regions for fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., Pho5, the promoters of the yeast α-mating factors, the polyhedron promoter of the baculovirus system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. Moreover, the vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should also be considered.

A recombinant nucleic acid of the present disclosure can be produced by ligating the cloned gene, or a portion thereof, into a vector suitable for expression in either prokaryotic cells, eukaryotic cells (yeast, avian, insect or mammalian), or both. Expression vehicles for production of a recombinant TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide include plasmids and other vectors. For instance, suitable vectors include plasmids of the following types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.

Some mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. Examples of other viral (including retroviral) expression systems can be found below in the description of gene therapy delivery systems. The various methods employed in the preparation of the plasmids and in transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see, e.g., Molecular Cloning A Laboratory Manual, 3rd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 2001). In some instances, it may be desirable to express the recombinant polypeptides by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUW1), and pBlueBac-derived vectors (such as the β-gal containing pBlueBac III).

In a preferred embodiment, a vector will be designed for production of the subject TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides in CHO cells, such as a Pcmv-Script vector (Stratagene, La Jolla, Calif.), pcDNA4 vectors (Invitrogen, Carlsbad, Calif.) and pCI-neo vectors (Promega, Madison, Wis.). As will be apparent, the subject gene constructs can be used to cause expression of the subject TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides in cells propagated in culture, e.g., to produce proteins, including fusion proteins or variant proteins, for purification.

This disclosure also pertains to a host cell transfected with a recombinant gene including a coding sequence for one or more of the subject TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides. The host cell may be any prokaryotic or eukaryotic cell. For example, a TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide of the disclosure may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells [e.g., a Chinese hamster ovary (CHO) cell line]. Other suitable host cells are known to those skilled in the art.

Accordingly, the present disclosure further pertains to methods of producing the subject TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides. For example, a host cell transfected with an expression vector encoding a TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide can be cultured under appropriate conditions to allow expression of the TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide to occur. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptide. Alternatively, the TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide may be isolated from a cytoplasmic or membrane fraction obtained from harvested and lysed cells. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The subject polypeptides can be isolated from cell culture medium, host cells, or both, using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, immunoaffinity purification with antibodies specific for particular epitopes of the TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides and affinity purification with an agent that binds to a domain fused to TGFβ superfamily type I receptor polypeptides, type II receptor polypeptides, and/or co-receptor polypeptides (e.g., a protein A column may be used to purify a TGFβ superfamily type I receptor-Fc fusion protein, type II receptor-Fc fusion protein, and/or co-receptor-Fc fusion protein). In some embodiments, the TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide is a fusion protein containing a domain which facilitates its purification.

In some embodiments, purification is achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange. A TGFβ superfamily type I receptor-Fc fusion protein, type II receptor-Fc fusion protein, and/or co-receptor-Fc fusion protein may be purified to a purity of >90%, >95%, >96%, >98%, or >99% as determined by size exclusion chromatography and >90%, >95%, >96%, >98%, or >99% as determined by SDS PAGE. The target level of purity should be one that is sufficient to achieve desirable results in mammalian systems, particularly non-human primates, rodents (mice), and humans.

In another embodiment, a fusion gene coding for a purification leader sequence, such as a poly-(His)/enterokinase cleavage site sequence at the N-terminus of the desired portion of the recombinant TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide, can allow purification of the expressed fusion protein by affinity chromatography using a Ni²⁺ metal resin. The purification leader sequence can then be subsequently removed by treatment with enterokinase to provide the purified TGFβ superfamily type I receptor polypeptide, type II receptor polypeptide, and/or co-receptor polypeptide. See, e.g., Hochuli et al. (1987) J. Chromatography 411:177; and Janknecht et al. (1991) PNAS USA 88:8972.

Techniques for making fusion genes are well known. Essentially, the joining of various DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed to generate a chimeric gene sequence. See, e.g., Current Protocols in Molecular Biology, eds. Ausubel et al., John Wiley & Sons: 1992.

4. Antibody Antagonists

In certain aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses disclosed herein is an antibody (activin and/or GDF antagonist antibody), or combination of antibodies. An activin and/or GDF antagonist antibody, or combination of antibodies, may bind to, for example, one or more ActRII ligands (e.g., activin (such as activin A, activin B, activin C, activin E, activin AB, activin AC, activin AE, activin BC, and/or activin BE), GDF8, GDF3, GDF1, GDF11, Nodal, and/or GDF3), ActRII receptors (ActRIIA and/or ActRIIB), type I receptors (ALK4, ALK5, and/or ALK7), and/or their co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). As described herein, activin and/or GDF antagonist antibodies may be used, alone or in combination with one or more supportive therapies or active agents, to treat or reduce the progression rate, frequency, and/or severity of kidney diseases, particularly treating, preventing or reducing the progression rate, frequency, and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, and/or activin BE). Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least activin. As used herein, an activin antibody (or anti-activin antibody) generally refers to an antibody that binds to activin with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting activin. In certain embodiments, the extent of binding of an activin antibody to an unrelated, non-activin protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to activin as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, an activin antibody binds to an epitope of activin that is conserved among activin from different species. In certain preferred embodiments, an anti-activin antibody binds to human activin. In some embodiments, an activin antibody may inhibit activin from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit activin-mediated signaling (e.g., Smad signaling). In some embodiments, an activin antibody may inhibit activin from binding to an ActRII co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B) and thus inhibit activin-mediated signaling (e.g., Smad signaling). It should be noted that activin A has similar sequence homology to activin B and therefore antibodies that bind to activin A, in some instances, may also bind to and/or inhibit activin B, which also applies to anti-activin B antibodies. In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to activin and further binds to, for example, one or more additional GDF ligands (e.g., GDF11, GDF8, GDF3, GDF1 and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to activin does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an activin antibody and one or more additional antibodies that bind to, for example, one or more additional GDF superfamily ligands (e.g., GDF8, GDF11, GDF3, GDF1 and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises an activin A antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least GDF8. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least GDF8. As used herein, a GDF8 antibody (or anti-GDF8 antibody) generally refers to an antibody that binds to GDF8 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting GDF8. In certain embodiments, the extent of binding of a GDF8 antibody to an unrelated, non-GDF8 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to GDF8 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, a GDF8 antibody binds to an epitope of GDF8 that is conserved among GDF8 from different species. In certain preferred embodiments, an anti-GDF8 antibody binds to human GDF8. In some embodiments, a GDF8 antibody may inhibit GDF8 from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit GDF8-mediated signaling (e.g., Smad signaling). In some embodiments, a GDF8 antibody may inhibit GDF8 from binding to a co-receptor and thus inhibit GDF8-mediated signaling (e.g., Smad signaling). It should be noted that GDF8 has high sequence homology to GDF11 and therefore antibodies that bind to GDF8, in some instances, may also bind to and/or inhibit GDF11. In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to GDF8 and further binds to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF11, GDF3, GDF1 and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to GDF8 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises a GDF8 antibody and one or more additional antibodies that bind to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF11, GDF3, GDF1, and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises a GDF8 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least GDF11. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least GDF11. As used herein, a GDF11 antibody (or anti-GDF11 antibody) generally refers to an antibody that binds to GDF11 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting GDF11. In certain embodiments, the extent of binding of a GDF11 antibody to an unrelated, non-GDF11 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to GDF11 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, a GDF11 antibody binds to an epitope of GDF11 that is conserved among GDF11 from different species. In certain preferred embodiments, an anti-GDF11 antibody binds to human GDF11. In some embodiments, a GDF11 antibody may inhibit GDF11 from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit GDF11-mediated signaling (e.g., Smad signaling). In some embodiments, a GDF11 antibody may inhibit GDF11 from binding to a co-receptor and thus inhibit GDF11-mediated signaling (e.g., Smad signaling). It should be noted that GDF11 has high sequence homology to GDF8 and therefore antibodies that bind to GDF11, in some instances, may also bind to and/or inhibit GDF8. In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to GDF11 and further binds to, for example, one or more additional GDF ligands [e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF3, GDF1 and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to GDF11 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises a GDF11 antibody and one or more additional antibodies that bind to, for example, one or more additional GDF ligands [e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF3, GDF1 and/or Nodal], one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises a GDF11 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least GDF1. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least GDF1. As used herein, a GDF1 antibody (or anti-GDF1 antibody) generally refers to an antibody that can bind to GDF1 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting GDF1. In certain embodiments, the extent of binding of a GDF1 antibody to an unrelated, non-GDF1 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to GDF1 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, a GDF1 antibody binds to an epitope of GDF1 that is conserved among GDF1 from different species. In certain preferred embodiments, an anti-GDF1 antibody binds to human GDF1. In some embodiments, a GDF1 antibody may inhibit GDF1 from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit GDF1-mediated signaling (e.g., Smad signaling). In some embodiments, a GDF1 antibody may inhibit GDF1 from binding to a co-receptor and thus inhibit GDF1-mediated signaling (e.g., Smad signaling). In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to GDF1 and further binds to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF3, Nodal, and/or GDF11), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B. In some embodiments, a multispecific antibody that binds to GDF1 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises a GDF1 antibody and one or more additional antibodies that bind to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF11, GDF3, and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises a GDF1 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least GDF3. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least GDF3. As used herein, a GDF3 antibody (or anti-GDF3 antibody) generally refers to an antibody that can bind to GDF3 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting GDF3. In certain embodiments, the extent of binding of a GDF3 antibody to an unrelated, non-GDF3 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to GDF3 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, a GDF3 antibody binds to an epitope of GDF3 that is conserved among GDF3 from different species. In certain preferred embodiments, an anti-GDF3 antibody binds to human GDF3. In some embodiments, a GDF3 antibody may inhibit GDF3 from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit GDF3-mediated signaling (e.g., Smad signaling). In some embodiments, a GDF3 antibody may inhibit GDF3 from binding to a co-receptor and thus inhibit GDF3-mediated signaling (e.g., Smad signaling). In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to GDF3 and further binds to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF1, Nodal, and/or GDF11), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to GDF3 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises a GDF3 antibody and one or more additional antibodies that bind to, for example, one or more additional GDF ligands [e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, activin BE), GDF8, GDF11, GDF1 and/or Nodal), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises a GDF3 antibody does not comprise an activin B antibody

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least Nodal. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least Nodal. As used herein, a Nodal antibody (or anti-Nodal antibody) generally refers to an antibody that can bind to Nodal with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting Nodal. In certain embodiments, the extent of binding of a Nodal antibody to an unrelated, non-Nodal protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to Nodal as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein interaction or binding affinity assay. In certain embodiments, a Nodal antibody binds to an epitope of Nodal that is conserved among Nodal from different species. In certain preferred embodiments, an anti-Nodal antibody binds to human Nodal. In some embodiments, a Nodal antibody may inhibit Nodal from binding to a type I and/or type II receptor (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7) and thus inhibit Nodal-mediated signaling (e.g., Smad signaling). In some embodiments, a Nodal antibody may inhibit Nodal from binding to a co-receptor and thus inhibit Nodal-mediated signaling (e.g., Smad signaling). In some embodiments, the disclosure relates to a multispecific antibody (e.g., bi-specific antibody), and uses thereof, that binds to Nodal and further binds to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF8, GDF11, GDF3, and/or GDF1), one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B. In some embodiments, a multispecific antibody that binds to Nodal does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises a Nodal antibody and one or more additional antibodies that bind to, for example, one or more additional GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF8, GDF3, GDF1 andor GDF11], one or more type I receptor and/or type II receptors (e.g., ActRIIA, ActRIIB, ALK4, ALK5, and/or ALK7), and/or one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B). In some embodiments, a combination of antibodies that comprises a Nodal antibody does not comprise activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least ActRIIB. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least ActRIIB. As used herein, an ActRIIB antibody (anti-ActRIIB antibody) generally refers to an antibody that binds to ActRIIB with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting ActRIIB. In certain embodiments, the extent of binding of an anti-ActRIIB antibody to an unrelated, non-ActRIIB protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to ActRIIB as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-ActRIIB antibody binds to an epitope of ActRIIB that is conserved among ActRIIB from different species. In certain preferred embodiments, an anti-ActRIIB antibody binds to human ActRIIB. In some embodiments, an anti-ActRIIB antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF8, GDF3, GDF1, and/or Nodal) from binding to ActRIIB. In some embodiments, an anti-ActRIIB antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to ActRIIB and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, and/or activin BE), GDF3, GDF1, and/or Nodal], type I receptor (e.g., ALK4, ALK5, and/or ALK7), one or more co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or an additional type II receptor (e.g., ActRIIA). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-ActRIIB antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF1, GDF3, and/or Nodal, co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), type I receptors (e.g., ALK4, ALK5, and/or ALK7), and/or additional type II receptors (e.g., ActRIIA). It should be noted that ActRIIB has sequence similarity to ActRIIA and therefore antibodies that bind to ActRIIB, in some instances, may also bind to and/or inhibit ActRIIA. In some embodiments, a multispecific antibody that binds to ActRIIB does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises an ActRIIB antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least ActRIIA. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least ActRIIA. As used herein, an ActRIIA antibody (anti-ActRIIA antibody) generally refers to an antibody that binds to ActRIIA with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting ActRIIA. In certain embodiments, the extent of binding of an anti-ActRIIA antibody to an unrelated, non-ActRIIA protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to ActRIIA as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-ActRIIA antibody binds to an epitope of ActRIIA that is conserved among ActRIIA from different species. In certain preferred embodiments, an anti-ActRIIA antibody binds to human ActRIIA. In some embodiments, an anti-ActRIIA antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to ActRIIA. In some embodiments, an anti-ActRIIA antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to ActRIIA and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type I receptor (e.g., ALK4, ALK5, and/or ALK7), co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or an additional type II receptor (e.g., ActRIIB). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-ActRIIA antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF1, GDF3, and/or Nodal, co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), type I receptors (e.g., ALK4, ALK5, and/or ALK7), and/or additional type II receptors (e.g., ActRIIB). It should be noted that ActRIIA has sequence similarity to ActRIIB and therefore antibodies that bind to ActRIIA, in some instances, may also bind to and/or inhibit ActRIIB. In some embodiments, a multispecific antibody that binds to ActRIIA does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises an ActRIIA antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least ALK4. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least ALK4. As used herein, an ALK4 antibody (anti-ALK4 antibody) generally refers to an antibody that binds to ALK4 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting ALK4. In certain embodiments, the extent of binding of an anti-ALK4 antibody to an unrelated, non-ALK4 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK4 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-ALK4 antibody binds to an epitope of ALK4 that is conserved among ALK4 from different species. In certain preferred embodiments, an anti-ALK4 antibody binds to human ALK4. In some embodiments, an anti-ALK4 antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to ALK4. In some embodiments, an anti-ALK4 antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to ALK4 and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type II receptor (e.g., ActRIIA and/or ActRIIB), co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or an additional type I receptor (e.g., ALK5 and/or ALK7). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-ALK4 antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF1, GDF3, and/or Nodal), co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), type II receptors (e.g., ActRIIA and/or ActRIIB), and/or additional type I receptors (e.g., ALK5 and/or ALK7). In some embodiments, a multispecific antibody that binds to ALK4 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises an ALK4 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least ALK5. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least ALK5. As used herein, an ALK5 antibody (anti-ALK5 antibody) generally refers to an antibody that binds to ALK5 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting ALK5. In certain embodiments, the extent of binding of an anti-ALK5 antibody to an unrelated, non-ALK5 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK5 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-ALK5 antibody binds to an epitope of ALK5 that is conserved among ALK5 from different species. In certain preferred embodiments, an anti-ALK5 antibody binds to human ALK5. In some embodiments, an anti-ALK5 antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to ALK5. In some embodiments, an anti-ALK5 antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to ALK5 and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type II receptor (e.g., ActRIIA and/or ActRIIB), co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or an additional type I receptor (e.g., ALK4 and/or ALK7). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-ALK5 antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF3, GDF1, and/or Nodal), co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), type II receptors (e.g., ActRIIA and/or ActRIIB), and/or additional type I receptors (e.g., ALK4 and/or ALK7). In some embodiments, a multispecific antibody that binds to ALK5 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises an ALK5 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least ALK7. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least ALK7. As used herein, an ALK7 antibody (anti-ALK7 antibody) generally refers to an antibody that binds to ALK7 with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting ALK7. In certain embodiments, the extent of binding of an anti-ALK7 antibody to an unrelated, non-ALK7 protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to ALK7 as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-ALK7 antibody binds to an epitope of ALK7 that is conserved among ALK7 from different species. In certain preferred embodiments, an anti-ALK7 antibody binds to human ALK7. In some embodiments, an anti-ALK7 antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to ALK7. In some embodiments, an anti-ALK7 antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to ALK7 and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type II receptor (e.g., ActRIIA and/or ActRIIB), co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or an additional type I receptor (e.g., ALK4 and/or ALK5). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-ALK7 antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF3, GDF1, and/or Nodal), co-receptors (e.g., Cripto, Cryptic, and/or Cryptic 1B), type II receptors (e.g., ActRIIA and/or ActRIIB), and/or additional type I receptors (e.g., ALK4 and/or ALK5). In some embodiments, a multispecific antibody that binds to ALK7 does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises an ALK7 antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least Cripto. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least Cripto. As used herein, a Cripto antibody (anti-Cripto antibody) generally refers to an antibody that binds to Cripto with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting Cripto. In certain embodiments, the extent of binding of an anti-Cripto antibody to an unrelated, non-Cripto protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to Cripto as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-Cripto antibody binds to an epitope of Cripto that is conserved among Cripto from different species. In certain preferred embodiments, an anti-Cripto antibody binds to human Cripto. In some embodiments, an anti-Cripto antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to Cripto. In some embodiments, an anti-Cripto antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to Cripto and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), one or more type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cryptic and/or Cryptic 1B). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-Cripto antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF3, GDF1, and/or Nodal), type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cryptic and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to Cripto does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises a Cripto antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least Cryptic. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least Cryptic. As used herein, a Cryptic antibody (anti-Cryptic antibody) generally refers to an antibody that binds to Cryptic with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting Cryptic. In certain embodiments, the extent of binding of an anti-Cryptic antibody to an unrelated, non-Cryptic protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to Cryptic as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-Cryptic antibody binds to an epitope of Cryptic that is conserved among Cryptic from different species. In certain preferred embodiments, an anti-Cryptic antibody binds to human Cryptic. In some embodiments, an anti-Cryptic antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to Cryptic. In some embodiments, an anti-Cryptic antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to Cryptic and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cripto and/or Cryptic 1B). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-Cryptic antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF3, GDF1, and/or Nodal), type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cripto and/or Cryptic 1B). In some embodiments, a multispecific antibody that binds to Cryptic does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises a Cryptic antibody does not comprise an activin B antibody.

In certain aspects, an activin and/or GDF antagonist antibody, or combination of antibodies, is an antibody that inhibits at least Cryptic 1B. Therefore, in some embodiments, an activin and/or GDF antagonist antibody, or combination of antibodies, binds to at least Cryptic 1B. As used herein, a Cryptic 1B antibody (anti-Cryptic 1B antibody) generally refers to an antibody that binds to Cryptic 1B with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting Cryptic 1B. In certain embodiments, the extent of binding of an anti-Cryptic 1B antibody to an unrelated, non-Cryptic 1B protein is less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or less than about 1% of the binding of the antibody to Cryptic 1B as measured, for example, by a radioimmunoassay (RIA), Biacore, or other protein-protein interaction or binding affinity assay. In certain embodiments, an anti-Cryptic 1B antibody binds to an epitope of Cryptic 1B that is conserved among Cryptic 1B from different species. In certain preferred embodiments, an anti-Cryptic 1B antibody binds to human Cryptic 1B. In some embodiments, an anti-Cryptic 1B antibody may inhibit one or more GDF ligands (e.g., GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF11, GDF1, GDF3, and/or Nodal) from binding to Cryptic 1B. In some embodiments, an anti-Cryptic 1B antibody is a multispecific antibody (e.g., bi-specific antibody) that binds to Cryptic 1B and one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC), GDF3, GDF1, and/or Nodal), type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cripto and/or Cryptic). In some embodiments, the disclosure relates to combinations of antibodies, and uses thereof, wherein the combination of antibodies comprises an anti-Cryptic 1B antibody and one or more additional antibodies that bind to, for example, one or more GDF ligands (e.g., GDF11, GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and activin BE), GDF3, GDF1, and/or Nodal), type II receptors (e.g., ActRIIA and/or ActRIIB), type I receptors (e.g., ALK4, ALK7, and/or ALK5), and/or an additional co-receptor (e.g., Cripto and/or Cryptic). In some embodiments, a multispecific antibody that binds to Cryptic 1B does not bind or does not substantially bind to activin B (e.g., binds to activin B with a K_(D) of greater than 1×10⁻⁷ M or has relatively modest binding, e.g., about 1×10⁻⁸ M or about 1×10⁻⁹ M). In some embodiments, a combination of antibodies that comprises a Cryptic 1B antibody does not comprise an activin B antibody.

The term antibody is used herein in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity. An antibody fragment refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds. Examples of antibody fragments include, but are not limited to, Fv, Fab, Fab′, Fab′-SH, F(ab′)₂; diabodies; linear antibodies; single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments [see, e.g., Hudson et al. (2003) Nat. Med. 9:129-134; Plückthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., (Springer-Verlag, New York), pp. 269-315 (1994); WO 93/16185; and U.S. Pat. Nos. 5,571,894; 5,587,458; and 5,869,046]. Diabodies are antibody fragments with two antigen-binding sites that may be bivalent or bispecific [see, e.g., EP 404,097; WO 1993/01161; Hudson et al. (2003) Nat. Med. 9:129-134 (2003); and Hollinger et al. (1993) Proc. Natl. Acad. Sci. USA 90: 6444-6448]. Triabodies and tetrabodies are also described in Hudson et al. (2003) Nat. Med. 9:129-134. Single-domain antibodies are antibody fragments comprising all or a portion of the heavy-chain variable domain or all or a portion of the light-chain variable domain of an antibody. In certain embodiments, a single-domain antibody is a human single-domain antibody (see, e.g., U.S. Pat. No. 6,248,516). Antibodies disclosed herein may be polyclonal antibodies or monoclonal antibodies. In certain embodiments, the antibodies of the present disclosure comprise a label attached thereto and able to be detected (e.g., the label can be a radioisotope, fluorescent compound, enzyme, or enzyme co-factor). In certain preferred embodiments, the antibodies of the present disclosure are isolated antibodies. In certain preferred embodiments, the antibodies of the present disclosure are recombinant antibodies.

The antibodies herein may be of any class. The class of an antibody refers to the type of constant domain or constant region possessed by its heavy chain. There are five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), for example, IgG₁, IgG₂, IgG₃, IgG₄, IgA₁, and IgA₂. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu.

In general, an antibody for use in the methods disclosed herein specifically binds to its target antigen, preferably with high binding affinity. Affinity may be expressed as a K_(D) value and reflects the intrinsic binding affinity (e.g., with minimized avidity effects). Typically, binding affinity is measured in vitro, whether in a cell-free or cell-associated setting. Any of a number of assays known in the art, including those disclosed herein, can be used to obtain binding affinity measurements including, for example, Biacore, radiolabeled antigen-binding assay (RIA), and ELISA. In some embodiments, antibodies of the present disclosure bind to their target antigens (e.g., ActRIIB, ActRIIA, ALK4, ALK5, ALK7, activin, GDF11, GDF8, GDF3, GDF1, Nodal, Cryptic, Cryptic 1B, and/or Cripto) with at least a K_(D) of 1×10⁻⁷ or stronger, 1×10⁻⁸ or stronger, 1×10⁻⁹ or stronger, 1×10⁻¹⁰ or stronger, 1×10⁻¹¹ or stronger, 1×10⁻¹² or stronger, 1×10⁻¹³ or stronger, or 1×10⁻¹⁴ or stronger.

In certain embodiments, K_(D) is measured by RIA performed with the Fab version of an antibody of interest and its target antigen as described by the following assay. Solution binding affinity of Fabs for the antigen is measured by equilibrating Fab with a minimal concentration of radiolabeled antigen (e.g.,¹²⁵I-labeled) in the presence of a titration series of unlabeled antigen, then capturing bound antigen with an anti-Fab antibody-coated plate [see, e.g., Chen et al. (1999) J. Mol. Biol. 293:865-881]. To establish conditions for the assay, multi-well plates (e.g., MICROTITER® from Thermo Scientific) are coated (e.g., overnight) with a capturing anti-Fab antibody (e.g., from Cappel Labs) and subsequently blocked with bovine serum albumin, preferably at room temperature (approximately 23° C.). In a non-adsorbent plate, radiolabeled antigen are mixed with serial dilutions of a Fab of interest [e.g., consistent with assessment of the anti-VEGF antibody, Fab-12, in Presta et al., (1997) Cancer Res. 57:4593-4599]. The Fab of interest is then incubated, preferably overnight but the incubation may continue for a longer period (e.g., about 65 hours) to ensure that equilibrium is reached. Thereafter, the mixtures are transferred to the capture plate for incubation, preferably at room temperature for about one hour. The solution is then removed and the plate is washed times several times, preferably with polysorbate 20 and PBS mixture. When the plates have dried, scintillant (e.g., MICROSCINT® from Packard) is added, and the plates are counted on a gamma counter (e.g., TOPCOUNT® from Packard).

According to another embodiment, K_(D) is measured using surface plasmon resonance assays using, for example a BIACORE® 2000 or a BIACORE® 3000 (BIAcore, Inc., Piscataway, N.J.) with immobilized antigen CM5 chips at about 10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIACORE, Inc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to the supplier's instructions. For example, an antigen can be diluted with 10 mM sodium acetate, pH 4.8, to 5 μg/ml (about 0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1 M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% polysorbate 20 (TWEEN-20®) surfactant (PBST) at at a flow rate of approximately 25 μl/min. Association rates (k_(on)) and dissociation rates (k_(off)) are calculated using, for example, a simple one-to-one Langmuir binding model (BIACORE® Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgrams. The equilibrium dissociation constant (K_(D)) is calculated as the ratio k_(off)/k_(on) (see, e.g., Chen et al., (1999) J. Mol. Biol. 293:865-881). If the on-rate exceeds, for example, 10⁶ M⁻¹ s⁻¹ by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (e.g., excitation=295 nm; emission=340 nm, 16 nm band-pass) of a 20 nM anti-antigen antibody (Fab form) in PBS in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophotometer (Aviv Instruments) or a 8000-series SLM-AMINCO® spectrophotometer (ThermoSpectronic) with a stirred cuvette.

Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g., E. coli or phage), as described herein. The nucleic acid and amino acid sequences of human ActRIIA, ActRIIB, ALK4, ALK5, ALK7, activin (activin A, activin B, activin C, activin E, activin AC, activin AB, activin BC, activin BE, and/or activin AE), GDF11, GDF8, GDF1, GDF3, Nodal, Cryptic, Cryptic 1B, and Cripto are known in the art. In addition, numerous methods for generating antibodies are well known in the art, some of which are described herein. Therefore antibody antagonists for use in accordance with this disclosure may be routinely made by the skilled person in the art based on the knowledge in the art and teachings provided herein.

In certain embodiments, an antibody provided herein is a chimeric antibody. A chimeric antibody refers to an antibody in which a portion of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species. Certain chimeric antibodies are described, for example, in U.S. Pat. No. 4,816,567; and Morrison et al., (1984) Proc. Natl. Acad. Sci. USA, 81:6851-6855. In some embodiments, a chimeric antibody comprises a non-human variable region (e.g., a variable region derived from a mouse, rat, hamster, rabbit, or non-human primate, such as a monkey) and a human constant region. In some embodiments, a chimeric antibody is a “class switched” antibody in which the class or subclass has been changed from that of the parent antibody. In general, chimeric antibodies include antigen-binding fragments thereof.

In certain embodiments, a chimeric antibody provided herein is a humanized antibody. A humanized antibody refers to a chimeric antibody comprising amino acid residues from non-human hypervariable regions (HVRs) and amino acid residues from human framework regions (FRs). In certain embodiments, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the HVRs (e.g., CDRs) correspond to those of a non-human antibody, and all or substantially all of the FRs correspond to those of a human antibody. A humanized antibody optionally may comprise at least a portion of an antibody constant region derived from a human antibody. A “humanized form” of an antibody, e.g., a non-human antibody, refers to an antibody that has undergone humanization. Humanized antibodies and methods of making them are reviewed, for example, in Almagro and Fransson (2008) Front. Biosci. 13:1619-1633 and are further described, for example, in Riechmann et al., (1988) Nature 332:323-329; Queen et al. (1989) Proc. Nat'l Acad. Sci. USA 86:10029-10033; U.S. Pat. Nos. 5,821,337; 7,527,791; 6,982,321; and 7,087,409; Kashmiri et al., (2005) Methods 36:25-34 [describing SDR (a-CDR) grafting]; Padlan, Mol. Immunol. (1991) 28:489-498 (describing “resurfacing”); Dall'Acqua et al. (2005) Methods 36:43-60 (describing “FR shuffling”); Osbourn et al. (2005) Methods 36:61-68; and Klimka et al. Br. J. Cancer (2000) 83:252-260 (describing the “guided selection” approach to FR shuffling). Human framework regions that may be used for humanization include but are not limited to: framework regions selected using the “best-fit” method (see, e.g., Sims et al. (1993) J. Immunol. 151:2296); framework regions derived from the consensus sequence of human antibodies of a particular subgroup of light or heavy chain variable regions (see, e.g., Carter et al. (1992) Proc. Natl. Acad. Sci. USA, 89:4285; and Presta et al. (1993) J. Immunol., 151:2623); human processed (somatically mutated) framework regions or human germline framework regions (see, e.g., Almagro and Fransson (2008) Front. Biosci. 13:1619-1633); and framework regions derived from screening FR libraries (see, e.g., Baca et al., (1997) J. Biol. Chem. 272:10678-10684; and Rosok et al., (1996) J. Biol. Chem. 271:22611-22618).

In certain embodiments, an antibody provided herein is a human antibody. Human antibodies can be produced using various techniques known in the art. Human antibodies are described generally in van Dijk and van de Winkel (2008) Curr. Opin. Pharmacol. 5: 368-74 (2001) and Lonberg, Curr. Opin. Immunol. 20:450-459. For example, human antibodies may be prepared by administering an immunogen (e.g., a GDF11 polypeptide, an activin B polypeptide, an ActRIIA polypeptide, or an ActRIIB polypeptide) to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge. Such animals typically contain all or a portion of the human immunoglobulin loci, which replace the endogenous immunoglobulin loci, or which are present extrachromosomally or integrated randomly into the animal's chromosomes. In such transgenic animals, the endogenous immunoglobulin loci have generally been inactivated. For a review of methods for obtaining human antibodies from transgenic animals see, for example, Lonberg (2005) Nat. Biotech. 23:1117-1125; U.S. Pat. Nos. 6,075,181 and 6,150,584 (describing XENOMOUSE™ technology); U.S. Pat. No. 5,770,429 (describing HuMab® technology); U.S. Pat. No. 7,041,870 (describing K-M MOUSE® technology); and U.S. Patent Application Publication No. 2007/0061900 (describing VelociMouse® technology). Human variable regions from intact antibodies generated by such animals may be further modified, for example, by combining with a different human constant region.

Human antibodies provided herein can also be made by hybridoma-based methods. Human myeloma and mouse-human heteromyeloma cell lines for the production of human monoclonal antibodies have been described (see, e.g., Kozbor J. Immunol., (1984) 133: 3001; Brodeur et al. (1987) Monoclonal Antibody Production Techniques and Applications, pp. 51-63, Marcel Dekker, Inc., New York; and Boerner et al. (1991) J. Immunol., 147: 86). Human antibodies generated via human B-cell hybridoma technology are also described in Li et al., (2006) Proc. Natl. Acad. Sci. USA, 103:3557-3562. Additional methods include those described, for example, in U.S. Pat. No. 7,189,826 (describing production of monoclonal human IgM antibodies from hybridoma cell lines) and Ni, Xiandai Mianyixue (2006) 26(4):265-268 (2006) (describing human-human hybridomas). Human hybridoma technology (Trioma technology) is also described in Vollmers and Brandlein (2005) Histol. Histopathol., 20(3):927-937 (2005) and Vollmers and Brandlein (2005) Methods Find Exp. Clin. Pharmacol., 27(3):185-91. Human antibodies provided herein may also be generated by isolating Fv clone variable-domain sequences selected from human-derived phage display libraries. Such variable-domain sequences may then be combined with a desired human constant domain. Techniques for selecting human antibodies from antibody libraries are known in the art and described herein.

For example, antibodies of the present disclosure may be isolated by screening combinatorial libraries for antibodies with the desired activity or activities. A variety of methods are known in the art for generating phage display libraries and screening such libraries for antibodies possessing the desired binding characteristics. Such methods are reviewed, for example, in Hoogenboom et al. (2001) in Methods in Molecular Biology 178:1-37, O'Brien et al., ed., Human Press, Totowa, N.J. and further described, for example, in the McCafferty et al. (1991) Nature 348:552-554; Clackson et al., (1991) Nature 352: 624-628; Marks et al. (1992) J. Mol. Biol. 222:581-597; Marks and Bradbury (2003) in Methods in Molecular Biology 248:161-175, Lo, ed., Human Press, Totowa, N.J.; Sidhu et al. (2004) J. Mol. Biol. 338(2):299-310; Lee et al. (2004) J. Mol. Biol. 340(5):1073-1093; Fellouse (2004) Proc. Natl. Acad. Sci. USA 101(34):12467-12472; and Lee et al. (2004) J. Immunol. Methods 284(1-2): 119-132.

In certain phage display methods, repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage as described in Winter et al. (1994) Ann. Rev. Immunol., 12: 433-455. Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments. Libraries from immunized sources provide high-affinity antibodies to the immunogen (e.g., activin A) without the requirement of constructing hybridomas. Alternatively, the naive repertoire can be cloned (e.g., from human) to provide a single source of antibodies to a wide range of non-self and also self-antigens without any immunization as described by Griffiths et al. (1993) EMBO J, 12: 725-734. Finally, naive libraries can also be made synthetically by cloning unrearranged V-gene segments from stem cells, and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro, as described by Hoogenboom and Winter (1992) J. Mol. Biol., 227: 381-388. Patent publications describing human antibody phage libraries include, for example: U.S. Pat. No. 5,750,373, and U.S. Patent Publication Nos. 2005/0079574, 2005/0119455, 2005/0266000, 2007/0117126, 2007/0160598, 2007/0237764, 2007/0292936, and 2009/0002360.

In certain embodiments, an antibody provided herein is a multispecific antibody, for example, a bispecific antibody. Multispecific antibodies (typically monoclonal antibodies) that have binding specificities for at least two different epitopes (e.g., two, three, four, five, or six or more) on one or more (e.g., two, three, four, five, six or more) antigens.

Techniques for making multispecific antibodies include, but are not limited to, recombinant co-expression of two immunoglobulin heavy-chain/light-chain pairs having different specificities [see, e.g., Milstein and Cuello (1983) Nature 305: 537; International patent publication no. WO 93/08829; and Traunecker et al. (1991) EMBO J. 10: 3655, and U.S. Pat. No. 5,731,168 (“knob-in-hole” engineering)]. Multispecific antibodies may also be made by engineering electrostatic steering effects for making antibody Fc-heterodimeric molecules (see, e.g., WO 2009/089004A1); cross-linking two or more antibodies or fragments [see, e.g., U.S. Pat. No. 4,676,980; and Brennan et al. (1985) Science, 229: 81]; using leucine zippers to produce bispecific antibodies [see, e.g., Kostelny et al. (1992) J. Immunol., 148(5):1547-1553]; using “diabody” technology for making bispecific antibody fragments [see, e.g., Hollinger et al. (1993) Proc. Natl. Acad. Sci. USA, 90:6444-6448]; using single-chain Fv (sFv) dimers (see, e.g., Gruber et al. (1994) J. Immunol., 152:5368); and preparing trispecific antibodies (see, e.g., Tutt et al. (1991) J. Immunol. 147: 60. Multispecific antibodies can be prepared as full-length antibodies or antibody fragments. Engineered antibodies with three or more functional antigen-binding sites, including “Octopus antibodies,” are also included herein [see, e.g., US 2006/0025576A1].

In certain embodiments, an antibody disclosed herein is a monoclonal antibody. Monoclonal antibody refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g., containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different epitopes, each monoclonal antibody of a monoclonal antibody preparation is directed against a single epitope on an antigen. Thus, the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present methods may be made by a variety of techniques, including but not limited to the hybridoma method, recombinant DNA methods, phage-display methods, and methods utilizing transgenic animals containing all or part of the human immunoglobulin loci, such methods and other exemplary methods for making monoclonal antibodies being described herein.

For example, by using immunogens derived from activin, anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols [see, e.g., Antibodies: A Laboratory Manual ed. by Harlow and Lane (1988) Cold Spring Harbor Press: 1988]. A mammal, such as a mouse, hamster, or rabbit, can be immunized with an immunogenic form of the activin polypeptide, an antigenic fragment which is capable of eliciting an antibody response, or a fusion protein. Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. An immunogenic portion of a activin polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibody production and/or level of binding affinity.

Following immunization of an animal with an antigenic preparation of activin, antisera can be obtained and, if desired, polyclonal antibodies can be isolated from the serum. To produce monoclonal antibodies, antibody-producing cells (lymphocytes) can be harvested from an immunized animal and fused by standard somatic cell fusion procedures with immortalizing cells such as myeloma cells to yield hybridoma cells. Such techniques are well known in the art, and include, for example, the hybridoma technique (see, e.g., Kohler and Milstein (1975) Nature, 256: 495-497), the human B cell hybridoma technique (see, e.g., Kozbar et al. (1983) Immunology Today, 4:72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al. (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with an activin polypeptide, and monoclonal antibodies isolated from a culture comprising such hybridoma cells.

In certain embodiments, one or more amino acid modifications may be introduced into the Fc region of an antibody provided herein thereby generating an Fc region variant. The Fc region variant may comprise a human Fc region sequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g., a substitution, deletion, and/or addition) at one or more amino acid positions.

For example, the present disclosure contemplates an antibody variant that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half-life of the antibody in vivo is important yet certain effector functions (e.g., complement-dependent cytotoxicity (CDC) and antibody-dependent cellular cytotoxicity (ADCC)) are unnecessary or deleterious. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks FcγR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII and FcγRIII FcR expression on hematopoietic cells is summarized in, for example, Ravetch and Kinet (1991) Annu. Rev. Immunol. 9:457-492. Non-limiting examples of in vitro assays to assess ADCC activity of a molecule of interest are described in U.S. Pat. No. 5,500,362; Hellstrom, I. et al. (1986) Proc. Natl. Acad. Sci. USA 83:7059-7063]; Hellstrom, I et al. (1985) Proc. Natl. Acad. Sci. USA 82:1499-1502; U.S. Pat. No. 5,821,337; Bruggemann, M. et al. (1987) J. Exp. Med. 166:1351-1361. Alternatively, non-radioactive assays methods may be employed (e.g., ACTI™, non-radioactive cytotoxicity assay for flow cytometry; CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96® non-radioactive cytotoxicity assay, Promega, Madison, Wis.). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and natural killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, for example, in an animal model such as that disclosed in Clynes et al. (1998) Proc. Natl. Acad. Sci. USA 95:652-656. C1q binding assays may also be carried out to confirm that the antibody is unable to bind C1q and hence lacks CDC activity (see, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO 2005/100402). To assess complement activation, a CDC assay may be performed (see, e.g, Gazzano-Santoro et al. (1996) J. Immunol. Methods 202:163; Cragg, M. S. et al. (2003) Blood 101:1045-1052; and Cragg, M. S, and M. J. Glennie (2004) Blood 103:2738-2743). FcRn binding and in vivo clearance/half-life determinations can also be performed using methods known in the art [see, e.g., Petkova, S. B. et al. (2006) Intl. Immunol. 18(12):1759-1769]. Antibodies of the present disclosure with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Pat. No. 6,737,056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called “DANA” Fc mutant with substitution of residues 265 and 297 to alanine (U.S. Pat. No. 7,332,581).

In certain embodiments, it may be desirable to create cysteine engineered antibodies, e.g., “thioMAbs,” in which one or more residues of an antibody are substituted with cysteine residues. In particular embodiments, the substituted residues occur at accessible sites of the antibody. By substituting those residues with cysteine, reactive thiol groups are thereby positioned at accessible sites of the antibody and may be used to conjugate the antibody to other moieties, such as drug moieties or linker-drug moieties, to create an immunoconjugate, as described further herein. In certain embodiments, any one or more of the following residues may be substituted with cysteine: V205 (Kabat numbering) of the light chain; A118 (EU numbering) of the heavy chain; and S400 (EU numbering) of the heavy chain Fc region. Cysteine engineered antibodies may be generated as described, for example, in U.S. Pat. No. 7,521,541.

In addition, the techniques used to screen antibodies in order to identify a desirable antibody may influence the properties of the antibody obtained. For example, if an antibody is to be used for binding an antigen in solution, it may be desirable to test solution binding. A variety of different techniques are available for testing interactions between antibodies and antigens to identify particularly desirable antibodies. Such techniques include ELISAs, surface plasmon resonance binding assays (e.g., the Biacore binding assay, Biacore AB, Uppsala, Sweden), sandwich assays (e.g., the paramagnetic bead system of IGEN International, Inc., Gaithersburg, Md.), western blots, immunoprecipitation assays, and immunohistochemistry.

In certain embodiments, amino acid sequence variants of the antibodies and/or the binding polypeptides provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the antibody and/or binding polypeptide. Amino acid sequence variants of an antibody and/or binding polypeptides may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the antibody and/or binding polypeptide, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody and/or binding polypeptide. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., target-binding (e.g., and activin such as activin E and/or activin C binding).

Alterations (e.g., substitutions) may be made in HVRs, for example, to improve antibody affinity. Such alterations may be made in HVR “hotspots,” i.e., residues encoded by codons that undergo mutation at high frequency during the somatic maturation process [see, e.g., Chowdhury (2008) Methods Mol. Biol. 207:179-196 (2008)], and/or SDRs (a-CDRs), with the resulting variant VH or VL being tested for binding affinity. Affinity maturation by constructing and reselecting from secondary libraries has been described in the art [see, e.g., Hoogenboom et al., in Methods in Molecular Biology 178:1-37, O'Brien et al., ed., Human Press, Totowa, N.J., (2001). In some embodiments of affinity maturation, diversity is introduced into the variable genes chosen for maturation by any of a variety of methods (e.g., error-prone PCR, chain shuffling, or oligonucleotide-directed mutagenesis). A secondary library is then created. The library is then screened to identify any antibody variants with the desired affinity. Another method to introduce diversity involves HVR-directed approaches, in which several HVR residues (e.g., 4-6 residues at a time) are randomized. HVR residues involved in antigen binding may be specifically identified, e.g., using alanine scanning mutagenesis or modeling. CDR-H3 and CDR-L3 in particular are often targeted.

In certain embodiments, substitutions, insertions, or deletions may occur within one or more HVRs so long as such alterations do not substantially reduce the ability of the antibody to bind to the antigen. For example, conservative alterations (e.g., conservative substitutions as provided herein) that do not substantially reduce binding affinity may be made in HVRs. Such alterations may be outside of HVR “hotspots” or SDRs. In certain embodiments of the variant VH and VL sequences provided above, each HVR either is unaltered, or contains no more than one, two or three amino acid substitutions.

A useful method for identification of residues or regions of the antibody and/or the binding polypeptide that may be targeted for mutagenesis is called “alanine scanning mutagenesis” as described by Cunningham and Wells (1989) Science, 244:1081-1085. In this method, a residue or group of target residues (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) are identified and replaced by a neutral or negatively charged amino acid (e.g., alanine or polyalanine) to determine whether the interaction of the antibody-antigen is affected. Further substitutions may be introduced at the amino acid locations demonstrating functional sensitivity to the initial substitutions. Alternatively, or additionally, a crystal structure of an antigen-antibody complex is determined to identify contact points between the antibody and antigen. Such contact residues and neighboring residues may be targeted or eliminated as candidates for substitution. Variants may be screened to determine whether they contain the desired properties.

Amino acid sequence insertions include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal insertions include an antibody with an N-terminal methionyl residue. Other insertional variants of the antibody molecule include the fusion of the N- or C-terminus of the antibody to an enzyme (e.g., for ADEPT) or a polypeptide which increases the serum half-life of the antibody.

In certain embodiments, an antibody and/or binding polypeptide provided herein may be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available. The moieties suitable for derivatization of the antibody and/or binding polypeptide include but are not limited to water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, polypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody and/or binding polypeptide may vary, and if more than one polymer are attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody and/or binding polypeptide to be improved, whether the antibody derivative and/or binding polypeptide derivative will be used in a therapy under defined conditions.

6. Small Molecule Antagonists

In other aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses described herein is a small molecule (activin and/or GDF small molecule antagonist), or combination of small molecule antagonists. A GDF small molecule antagonist, or combination of small molecule antagonists, may inhibit, for example, one or more GDF ligands (e.g., activin.(e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF11, GDF8, GDF3, GDF1, and/or Nodal), a type I receptor (e.g., ALK4, ALK5, and/or ALK7), a type II receptor (e.g., ActRIIB and/or ActRIIA), a co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), and/or a Smad polypeptide (e.g., Smad2 and/or Smad3). In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits signaling mediated by one or more GDF ligands, for example, as determined in a cell-based assay such as those described herein. As described herein, GDF small molecule antagonists may be used, alone or in combination with one or more supportive therapies or active agents, to treat or reduce the progression rate, frequency, and/or severity of kidney diseases, particularly treating, preventing or reducing the progression rate, frequency, and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least GDF11, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least GDF8, optionally further inhibiting one or more of GDF11, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least activin (activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), optionally further inhibiting one or more of GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least activin B, optionally further inhibiting one or more of activin (e.g., activin A, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least activin A, optionally further inhibiting one or more of activin (e.g., activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least GDF1, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF11, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Nodal, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF1, GDF11, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least GDF3, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Cripto, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Cryptic, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Cryptic 1B, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least ActRIIA, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic 1B, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least ActRIIB, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ALK4, ALK5, ALK7, Cripto, Cryptic 1B, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least ALK4, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK7, Cripto, Cryptic 1B, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least ALK5, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK7, Cripto, Cryptic 1B, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least ALK7, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK4, Cripto, Cryptic 1B, Cryptic, Smad2, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Smad2, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK4, ALK7, Cripto, Cryptic 1B, Cryptic, and Smad3. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, inhibits at least Smad3, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK5, ALK4, ALK7, Cripto, Cryptic 1B, Cryptic, and Smad2. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, as disclosed herein does not inhibit or does not substantially inhibit activin B. In some embodiments, a GDF small molecule antagonist, or combination of small molecule antagonists, as disclosed herein does not inhibit or does not substantially inhibit activin A. GDF small molecule antagonists can be direct or indirect inhibitors. For example, an indirect small molecule antagonist, or combination of small molecule antagonists, may inhibit the expression (e.g., transcription, translation, cellular secretion, or combinations thereof) of at least one or more GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, or activin BE), GDF11, GDF1, Nodal, GDF3, and/or GDF8), type I receptors (e.g., ALK4, ALK5, and/or ALK7), type II receptors (e.g., ActRIIA and/or ActRIIB), co-receptors (e.g., Cryptic, Cryptic 1B, and/or Cripto), and/or one or more downstream signaling components (e.g., Smads, such as Smad2 and Smad3). Alternatively, a direct small molecule antagonist, or combination of small molecule antagonists, may directly bind to and inhibit, for example, one or more one or more GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, or activin BE), GDF11, GDF1, Nodal, GDF3, and/or GDF8), type I receptor (e.g., ALK4, ALK5 and/or ALK7), type II receptors (e.g., ActRIIA and/or ActRIIB), co-receptors (e.g., Cryptic, Cryptic 1B, and/or Cripto), and/or one or more downstream signaling components (e.g., Smads, such as Smad2 and Smad3). Combinations of one or more indirect and one or more direct GDF small molecule antagonists may be used in accordance with the methods disclosed herein.

Binding organic small molecules of the present disclosure may be, for example, aldehydes, ketones, oximes, hydrazones, semicarbazones, carbazides, primary amines, secondary amines, tertiary amines, N-substituted hydrazines, hydrazides, alcohols, ethers, thiols, thioethers, disulfides, carboxylic acids, esters, amides, ureas, carbamates, carbonates, ketals, thioketals, acetals, thioacetals, aryl halides, aryl sulfonates, alkyl halides, alkyl sulfonates, aromatic compounds, heterocyclic compounds, anilines, alkenes, alkynes, diols, amino alcohols, oxazolidines, oxazolines, thiazolidines, thiazolines, enamines, sulfonamides, epoxides, aziridines, isocyanates, sulfonyl chlorides, diazo compounds, and acid chlorides.

7. Polynucleotide Antagonists

In other aspects, an activin and/or GDF antagonist to be used in accordance with the methods and uses disclosed herein is a polynucleotide (activin and/or GDF polynucleotide antagonist), or combination of polynucleotides. A GDF polynucleotide antagonist, or combination of polynucleotide antagonists, may inhibit, for example, one or more GDF ligands (e.g., activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE, or activin BE), GDF11, GDF8, GDF3, GDF1, and/or Nodal), type I receptors (e.g., ALK4, ALK5, and/or ALK7), type II receptors (e.g., ActRIIA and/or ActRIIB), co-receptors (e.g., Cryptic, Cryptic 1B, and/or Cripto), and/or one or more downstream signaling components (e.g., Smads, such as Smad2 and Smad3). In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits signaling mediated by one or more GDF ligands, for example, as determined in a cell-based assay such as those described herein. As described herein, GDF polynucleotide antagonists may be used, alone or in combination with one or more supportive therapies or active agents, to treat, or reduce the progression rate, frequency, and/or severity of kidney diseases, particularly treating, preventing or reducing the progression rate, frequency and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least GDF11, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least GDF8, optionally further inhibiting one or more of GDF11, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least activin (activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), optionally further inhibiting one or more of GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least activin A, optionally further inhibiting one or more of additional activin (e.g., activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least activin B, optionally further inhibiting one or more of additional activin (activin A, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least GDF1, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF11, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Nodal, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF3, GDF11, GDF1, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least GDF3, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF1, GDF11, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Cripto, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Cryptic, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto, Cryptic 1B, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Cryptic 1B, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least ActRIIA, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least ActRIIB, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIA, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least ALK4, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ActRIIA, ALK5, ALK7, Cryptic, Cryptic 1B, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least ALK5, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ActRIIA, ALK4, ALK7, Cryptic, Cryptic 1B, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least ALK7, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ActRIIA, ALK5, ALK4, Cryptic, Cryptic 1B, Cripto, Smad2, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Smad2, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ActRIIA, ALK5, ALK4, ALK7, Cryptic, Cryptic 1B, Cripto, and Smad3. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, inhibits at least Smad3, optionally further inhibiting one or more of GDF8, activin (e.g., activin A, activin B, activin C, activin E, activin AB, activin AC, activin BC, activin AE and/or activin BE), GDF11, GDF3, GDF1, Nodal, ActRIIB, ActRIIA, ALK5, ALK4, ALK7, Cryptic, Cryptic 1B, Cripto, and Smad2. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, as disclosed herein does not inhibit or does not substantially inhibit activin B. In some embodiments, a GDF polynucleotide antagonist, or combination of polynucleotide antagonists, as disclosed herein does not inhibit or does not substantially inhibit activin A.

In some embodiments, the polynucleotide antagonists of the disclosure may be an antisense nucleic acid, an RNAi molecule (e.g., small interfering RNA (siRNA), small-hairpin RNA (shRNA), microRNA (miRNA)), an aptamer and/or a ribozyme. The nucleic acid and amino acid sequences of human GDF11, GDF8, activin (activin A, activin B, activin C, and activin E), GDF1, Nodal, GDF3, ActRIIA, ActRIIB, Cryptic, Cryptic 1B, Cripto, ALK4, ALK5, ALK7, Smad2, and Smad3 are known in the art. In addition, many different methods of generating polynucleotide antagonists are well known in the art. Therefore polynucleotide antagonists for use in accordance with this disclosure may be routinely made by the skilled person in the art based on the knowledge in the art and teachings provided herein.

Antisense technology can be used to control gene expression through antisense DNA or RNA, or through triple-helix formation. Antisense techniques are discussed, for example, in Okano (1991) J. Neurochem. 56:560; Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple-helix formation is discussed in, for instance, Cooney et al. (1988) Science 241:456; and Dervan et al., (1991) Science 251:1300. The methods are based on binding of a polynucleotide to a complementary DNA or RNA. In some embodiments, the antisense nucleic acids comprise a single-stranded RNA or DNA sequence that is complementary to at least a portion of an RNA transcript of a gene disclosed herein. However, absolute complementarity, although preferred, is not required.

A sequence “complementary to at least a portion of an RNA,” referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acids of a gene disclosed herein, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid. Generally, the larger the hybridizing nucleic acid, the more base mismatches with an RNA it may contain and still form a stable duplex (or triplex as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

Polynucleotides that are complementary to the 5′ end of the message, for example, the 5′-untranslated sequence up to and including the AUG initiation codon, should work most efficiently at inhibiting translation. However, sequences complementary to the 3′-untranslated sequences of mRNAs have been shown to be effective at inhibiting translation of mRNAs as well (see, e.g., Wagner, R., (1994) Nature 372:333-335). Thus, oligonucleotides complementary to either the 5′- or 3′-non-translated, non-coding regions of a gene of the disclosure, could be used in an antisense approach to inhibit translation of an endogenous mRNA. Polynucleotides complementary to the 5′-untranslated region of the mRNA should include the complement of the AUG start codon. Antisense polynucleotides complementary to mRNA coding regions are less efficient inhibitors of translation but could be used in accordance with the methods of the present disclosure. Whether designed to hybridize to the 5′-, 3′- or coding region of an mRNA of the disclosure, antisense nucleic acids should be at least six nucleotides in length, and are preferably oligonucleotides ranging from 6 to about 50 nucleotides in length. In specific aspects the oligonucleotide is at least 10 nucleotides, at least 17 nucleotides, at least 25 nucleotides or at least 50 nucleotides.

In one embodiment, the antisense nucleic acid of the present disclosure is produced intracellularly by transcription from an exogenous sequence. For example, a vector or a portion thereof is transcribed, producing an antisense nucleic acid (RNA) of a gene of the disclosure. Such a vector would contain a sequence encoding the desired antisense nucleic acid. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in vertebrate cells. Expression of the sequence encoding desired genes of the instant disclosure, or fragments thereof, can be by any promoter known in the art to act in vertebrate, preferably human cells. Such promoters can be inducible or constitutive. Such promoters include, but are not limited to, the SV40 early promoter region [see, e.g., Benoist and Chambon (1981) Nature 290:304-310], the promoter contained in the 3′ long-terminal repeat of Rous sarcoma virus [see, e.g., Yamamoto et al. (1980) Cell 22:787-797], the herpes thymidine promoter [see, e.g., Wagner et al. (1981) Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445], and the regulatory sequences of the metallothionein gene [see, e.g., Brinster, et al. (1982) Nature 296:39-42].

In some embodiments, the polynucleotide antagonists are interfering RNA (RNAi) molecules that target the expression of one or more of: GDF11, GDF8, activin (activin A, activin B, activin C, and activin E), GDF1, GDF3, ActRIIA, ActRIIB, Cryptic, Cryptic 1B, Cripto, ALK4, ALK5, ALK7, Smad2, and Smad3 RNAi refers to the expression of an RNA which interferes with the expression of the targeted mRNA. Specifically, RNAi silences a targeted gene via interacting with the specific mRNA through a siRNA (small interfering RNA). The ds RNA complex is then targeted for degradation by the cell. An siRNA molecule is a double-stranded RNA duplex of 10 to 50 nucleotides in length, which interferes with the expression of a target gene which is sufficiently complementary (e.g., at least 80% identity to the gene). In some embodiments, the siRNA molecule comprises a nucleotide sequence that is at least 85, 90, 95, 96, 97, 98, 99, or 100% identical to the nucleotide sequence of the target gene.

Additional RNAi molecules include short-hairpin RNA (shRNA); also short-interfering hairpin and microRNA (miRNA). The shRNA molecule contains sense and antisense sequences from a target gene connected by a loop. The shRNA is transported from the nucleus into the cytoplasm, and it is degraded along with the mRNA. Pol III or U6 promoters can be used to express RNAs for RNAi. Paddison et al. (Genes & Dev. (2002) 16:948-958, 2002) have used small RNA molecules folded into hairpins as a means to affect RNAi. Accordingly, such short-hairpin RNA (shRNA) molecules are also advantageously used in the methods described herein. The length of the stem and loop of functional shRNAs varies; stem lengths can range anywhere from about 25 to about 30 nt, and loop size can range between 4 to about 25 nt without affecting silencing activity. While not wishing to be bound by any particular theory, it is believed that these shRNAs resemble the double-stranded RNA (dsRNA) products of the DICER RNase and, in any event, have the same capacity for inhibiting expression of a specific gene. The shRNA can be expressed from a lentiviral vector. An miRNA is a single-stranded RNA of about 10 to 70 nucleotides in length that are initially transcribed as pre-miRNA characterized by a “stem-loop” structure, which are subsequently processed into processed miRNA after further processing through the RISC.

Molecules that mediate RNAi, including without limitation siRNA, can be produced in vitro by chemical synthesis (Hohjoh, FEBS Lett 521:195-199, 2002), hydrolysis of dsRNA (Yang et al., Proc Natl Acad Sci USA 99:9942-9947, 2002), by in vitro transcription with T7 RNA polymerase (Donzeet et al., Nucleic Acids Res 30:e46, 2002; Yu et al., Proc Natl Acad Sci USA 99:6047-6052, 2002), and by hydrolysis of double-stranded RNA using a nuclease such as E. coli RNase III (Yang et al., Proc Natl Acad Sci USA 99:9942-9947, 2002).

According to another aspect, the disclosure provides polynucleotide antagonists including but not limited to, a decoy DNA, a double-stranded DNA, a single-stranded DNA, a complexed DNA, an encapsulated DNA, a viral DNA, a plasmid DNA, a naked RNA, an encapsulated RNA, a viral RNA, a double-stranded RNA, a molecule capable of generating RNA interference, or combinations thereof.

In some embodiments, the polynucleotide antagonists of the disclosure are aptamers. Aptamers are nucleic acid molecules, including double-stranded DNA and single-stranded RNA molecules, which bind to and form tertiary structures that specifically bind to a target molecule. The generation and therapeutic use of aptamers are well established in the art (see, e.g., U.S. Pat. No. 5,475,096). Additional information on aptamers can be found in U.S. Patent Application Publication No. 20060148748. Nucleic acid aptamers are selected using methods known in the art, for example via the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process. SELEX is a method for the in vitro evolution of nucleic acid molecules with highly specific binding to target molecules as described in, e.g., U.S. Pat. Nos. 5,475,096; 5,580,737; 5,567,588; 5,707,796; 5,763,177; 6,011,577; and 6,699,843. Another screening method to identify aptamers is described in U.S. Pat. No. 5,270,163. The SELEX process is based on the capacity of nucleic acids for forming a variety of two- and three-dimensional structures, as well as the chemical versatility available within the nucleotide monomers to act as ligands (form specific binding pairs) with virtually any chemical compound, whether monomeric or polymeric, including other nucleic acid molecules and polypeptides. Molecules of any size or composition can serve as targets. The SELEX method involves selection from a mixture of candidate oligonucleotides and step-wise iterations of binding, partitioning and amplification, using the same general selection scheme, to achieve desired binding affinity and selectivity. Starting from a mixture of nucleic acids, which can comprise a segment of randomized sequence, the SELEX method includes steps of contacting the mixture with the target under conditions favorable for binding; partitioning unbound nucleic acids from those nucleic acids which have bound specifically to target molecules; dissociating the nucleic acid-target complexes; amplifying the nucleic acids dissociated from the nucleic acid-target complexes to yield a ligand enriched mixture of nucleic acids. The steps of binding, partitioning, dissociating and amplifying are repeated through as many cycles as desired to yield nucleic acid ligands which bind with high affinity and specificity to the target molecule.

Typically, such binding molecules are separately administered to the animal [see, e.g., O'Connor (1991) J. Neurochem. 56:560], but such binding molecules can also be expressed in vivo from polynucleotides taken up by a host cell and expressed in vivo [see, e.g., Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)].

8. Follistatin and FLRG Antagonists

In other aspects, an activin and/or GDF antagonist is a follistatin or FLRG polypeptide. As described herein, follistatin and/or FLRG polypeptides may be used to treat or reduce the progression rate, frequency, and/or severity of kidney disease, particularly treating, preventing or reducing the progression rate, frequency, and/or severity of one or more kidney disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

The term “follistatin polypeptide” includes polypeptides comprising any naturally occurring polypeptide of follistatin as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity, and further includes any functional monomer or multimer of follistatin. In certain preferred embodiments, follistatin polypeptides of the disclosure bind to and/or inhibit activin activity, particularly activin A. Variants of follistatin polypeptides that retain activin binding properties can be identified based on previous studies involving follistatin and activin interactions. For example, WO2008/030367 discloses specific follistatin domains (“FSDs”) that are shown to be important for activin binding. As shown below in SEQ ID NOs: 150 and 151, the follistatin N-terminal domain, FSD2, and to a lesser extent FSD1 represent exemplary domains within follistatin that are important for activin binding. In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII polypeptides, and such methods also pertain to making and testing variants of follistatin. Follistatin polypeptides include polypeptides derived from the sequence of any known follistatin having a sequence at least about 80% identical to the sequence of a follistatin polypeptide, and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater identity. Examples of follistatin polypeptides include the processed follistatin polypeptide or shorter isoforms or other variants of the human follistatin precursor polypeptide as described, for example, in WO2005/025601.

Follistatin is a single-chain polypeptide that can have a range of molecular weights from 31 to 49 kDa based on alternative mRNA splicing and variable glycosylation of the protein. Alternatively spliced mRNAs from the follistatin gene encode isoforms of 288 amino acids (i.e., FST288, SEQ ID NO: 150) and 315 amino acids (i.e., FST315, SEQ ID NO: 151), and the latter can be processed proteolytically to yield yet another isoform, follistatin 303 (FST303). Analysis of the amino acid sequence of native human follistatin polypeptide has revealed that it comprises five domains: a signal sequence (amino acids 1-29 of SEQ ID NO: 150), an N-terminal domain (FST_(ND)) (amino acids 30-94 of SEQ ID NO: 150), follistatin domain-1 (FST_(FD1)) (amino acids 95-164 of SEQ ID NO: 150), follistatin domain-2 (FST_(FD2)) (amino acids (168-239 of SEQ ID NO:1), and follistatin domain-3 (FST_(FD3)) (amino acids 245-316 of SEQ ID NO: 150). See Shimanski et al (1988) Proc Natl Acad Sci USA 85:4218-4222.

The human follistatin-288 (FST288) precursor has the amino acid sequence of SEQ ID NO: 150 (NCBI Reference Sequence NP_006341; Uniprot P19883-2), with the signal peptide indicated by dotted underline, the N-terminal domain (FST_(ND)) indicated by dashed underline, and the follistatin domains 1-3 (FST_(FD1), FST_(FD2), FST_(FD3)) indicated by solid underline.

The Processed human follistatin variant FST288 has the amino acid sequence of SEQ ID NO: 152, with the N-terminal domain indicated by dashed underline and the follistatin domains 1-3 indicated by solid underline. Moreover, it will be appreciated that any of the initial amino acids G or N, prior to the first cysteine may be removed by processing or intentionally eliminated without any consequence, and polypeptides comprising such slightly smaller polypeptides are further included.

The human follistatin-315 (FST315) precursor has the amino acid sequence of SEQ ID NO: 151 (NCBI Reference Sequence NP_037541.1; Uniprot P19883), with the signal peptide indicated by dotted underline, the N-terminal domain (FST_(ND)) indicated by dashed underline, and the follistatin domains 1-3 (FST_(FD1), FST_(FD2), FST_(FD3)) indicated by solid underline. The last 27 residues which represent the C-terminal extension distinguish this follistatin isoform from the shorter follistatin isoform FST288.

Processed human FST315 has the amino acid sequence of SEQ ID NO: 153, with the N-terminal domain indicated by dashed underline and the follistatin domains 1-3 indicated by solid underline. Moreover, it will be appreciated that any of the initial amino acids G or N, prior to the first cysteine may be removed by processing or intentionally eliminated without any consequence, and polypeptides comprising such slightly shorter polypeptides are further included.

Follistatin-related polypeptides of the disclosure may include any naturally occurring domain of a follistatin protein as well as variants thereof (e.g., mutants, fragments, and peptidomimetic forms) that retain a useful activity. For example, it is well-known that FST315 and FST288 have high affinity for myostatin, activins (activin A and activin B), and GDF11 and that the follistatin domains (e.g., FST_(ND), FST_(FD1), FST_(FD2), and FST_(FD3)) are thought to be involved in the binding of such TGFβ ligands. However, there is evidence that each of these four domains has a different affinity for these TGF-β ligands. For example, a recent study has demonstrated that polypeptide constructs comprising only the N-terminal domain and two FST_(FD1) domains in tandem retained high affinity for myostatin, demonstrated little or no affinity for activins, and promoted systemic muscle growth when introduced into a mouse by gene expression (Nakatani et al (2008) FASEB 22:478-487). Accordingly, the present disclosure encompasses, in part, variant follistatin proteins that demonstrate selective binding and/or inhibition of a given TGFβ ligand relative to a naturally occurring FST protein (e.g., maintaining high-affinity for myostatin while having a significantly reduced affinity for activin).

An FST_(FD1) sequence may be advantageously maintained in structural context by expression as a polypeptide further comprising the FST_(ND) domain. Accordingly, the disclosure includes polypeptides comprising the FST_(ND)-FST_(FD1) sequence, as set forth in SEQ ID NO: 154, and, for example, one or more heterologous polypeptides, and moreover, it will be appreciated that any of the initial amino acids G or N, prior to the first cysteine may be removed by processing or intentionally eliminated without any consequence, and polypeptides comprising such slightly shorter polypeptides are further included.

As demonstrated by Nakatani et al., a FST_(ND)-FST_(FD1)-FST_(FD1) construct is sufficient to confer systemic muscle growth when genetically expressed in a mouse, and accordingly the disclosure includes polypeptides comprising the amino acid sequence of SEQ ID NO: 155 and, for example, one or more heterologous polypeptides.

While the FST_(FD1) sequence confers myostatin and GDF11 binding, it has been demonstrated that activins, particularly activin A but also activin B, are also negative regulators of muscle, and therefore a follistatin polypeptide that inhibits both the myostatin/GDF11 ligand group and the activin A/activin B ligand group may provide a more potent muscle effect. Given that FST_(FD2) confers activin A and B binding, the disclosure provides polypeptides comprising FST_(FD1)-FST_(FD2) (SEQ ID NO: 156) and FST_(FD1)-FST_(FD2)-FST_(FD3) (SEQ ID NO: 157), as well as constructs comprising FST_(ND)-FST_(FD1)-FST_(FD2) (SEQ ID NO: 158) and, for example, one or more heterologous polypeptides.

A follistatin polypeptide of 291 amino acids (representing a truncation of the naturally occurring FST315) may have advantageous properties in certain embodiments. Accordingly, unprocessed (SEQ ID NO: 159) and processed FST291 (SEQ ID NO: 160) polypeptides are included in the disclosure and may be combined with heterologous proteins. Moreover, it will be appreciated that any of the initial amino acids G or N, prior to the first cysteine may be removed by processing or intentionally eliminated without any consequence, and polypeptides comprising such slightly shorter polypeptides are further included.

Follistatin proteins herein may be referred to as FST. If followed by a number, such as FST288, this indicates that the protein is the 288-amino-acid isoform of follistatin. If presented as FST288-Fc, this indicates that an Fc domain is fused to the C-terminus of FST288, which may or may not include an intervening linker. The Fc in this instance may be any immunoglobulin Fc portion as that term is defined herein. If presented as FST288-G1Fc, this indicates that the Fc portion of human IgG1 is fused at the C-terminal of FST288. Unless indicated to the contrary, a protein described with this nomenclature will represent a human follistatin protein.

In other aspects, an agent for use in accordance with the methods disclosed herein is a follistatin-like related gene (FLRG), also known as follistatin-related protein 3 (FSTL3). The term “FLRG polypeptide” includes polypeptides comprising any naturally occurring polypeptide of FLRG as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. In certain preferred embodiments, FLRG polypeptides of the disclosure bind to and/or inhibit activin activity, particularly activin A. Variants of FLRG polypeptides that retain activin binding properties can be identified using routine methods to assay FLRG and activin interactions (see, e.g., U.S. Pat. No. 6,537,966). In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII polypeptides and such methods also pertain to making and testing variants of FLRG. FLRG polypeptides include polypeptides derived from the sequence of any known FLRG having a sequence at least about 80% identical to the sequence of an FLRG polypeptide, and optionally at least 85%, 90%, 95%, 97%, 99% or greater identity.

Closely related to the native follistatin isoforms encoded by FSTN is a naturally occurring protein encoded by the FSTL3 gene and known alternatively as follistatin-related gene (FLRG), follistatin-like 3 (FSTL3), or follistatin-related protein (FSRP) (Schneyer et al (2001) Mol Cell Endocrinol 180:33-38). Like follistatin, FLRG binds to myostatin, activins, and GDF11 with high affinity and thereby inhibits their bioactivity in vivo (Sidis et al (2006) Endocrinology 147:3586-3597). Unlike follistatin, FLRG does not possess a heparin-binding sequence, cannot bind to cell-surface proteoglycans, and therefore is a less potent inhibitor of activin than is FST288 in the immediate vicinity of the cell surface. In contrast to follistatin, FLRG also circulates in the blood bound to processed myostatin, and thus resembles myostatin propeptide in this regard (Hill et al (2002) J Biol Chem 277:40735-40741). Unlike follistatin, FLRG deficiency in mice is not lethal, although it does cause a variety of metabolic phenotypes (Mukherjee et al (2007) Proc Natl Acad Sci USA 104:1348-1353).

The overall structure of FLRG closely resembles that of follistatin. Native human FLRG precursor is a single-chain polypeptide which comprises four domains: a signal sequence (amino acids 1-26 of SEQ ID NO: 161), an N-terminal domain (FLRG_(ND)) (amino acids 38-96 of SEQ ID NO: 161, which interacts differently with myostatin compared with activin A (Cash et al (2012) J Biol Chem 287:1043-1053)), and two follistatin domains referred to herein as FLRG_(FD1) (amino acids 99-167 of SEQ ID NO: 161) and FLRG_(FD2) (amino acids 171-243 of SEQ ID NO: 161).

The term “FLRG polypeptide” is used to refer to polypeptides comprising any naturally occurring polypeptide of FLRG as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. In certain preferred embodiments, FLRG polypeptides of the disclosure bind to and/or inhibit activity of myostatin, GDF11, or activin, particularly activin A (e.g., ligand-mediated activation of ActRIIA and/or ActRIIB Smad2/3 signaling). Variants of FLRG polypeptides that retain ligand binding properties can be identified using routine methods to assay interactions between FLRG and ligands (see, e.g., U.S. Pat. No. 6,537,966). In addition, methods for making and testing libraries of polypeptides are described herein and such methods also pertain to making and testing variants of FLRG.

For example, FLRG polypeptides include polypeptides comprising an amino acid sequence derived from the sequence of any known FLRG having a sequence at least about 80% identical to the sequence of a FLRG polypeptide (for example, SEQ ID NOs: 161-164), and optionally at least 85%, 90%, 95%, 97%, 99% or greater identity to any of SEQ ID NOs: 161-164. The term “FLRG fusion polypeptide” may refer to fusion proteins that comprise any of the polypeptides mentioned above along with a heterologous (non-FLRG) portion. An amino acid sequence is understood to be heterologous to FLRG if it is not uniquely found in human FLRG, represented by SEQ ID NO: 161. Many examples of heterologous portions are provided herein, and such heterologous portions may be immediately adjacent, by amino acid sequence, to the FLRG polypeptide portion of a fusion protein, or separated by intervening amino acid sequence, such as a linker or other sequence.

The human FLRG precursor has the following amino acid sequence (SEQ ID NO: 161) (amino acids 1-263 of NCBI Reference Sequence NP_005851.1), with the signal peptide indicated by dotted underline, the N-terminal domain (FLRG_(ND)) indicated by dashed underline, and the two follistatin domains (FST_(FD1), FST_(FD2)) indicated by solid underline.

Processed human FLRG comprises the following amino acid sequence (SEQ ID NO: 162) (amino acids 38-263 of NCBI Reference Sequence NP_005851.1) with the N-terminal domain indicated by dashed underline and the two follistatin domains indicated by solid underline. Moreover, it will be appreciated that any of the amino acids (positions 27-37 of SEQ ID NO: 161) prior to the first cysteine (position 38 in SEQ ID NO: 161) may be included without substantial consequence, and polypeptides comprising such slightly longer polypeptides are included.

A FLRG_(FD) sequence may be advantageously maintained in structural context by expression as a polypeptide further comprising the FLRG_(ND) domain. Accordingly, the disclosure includes polypeptides comprising the FLRG_(ND)-FLRG_(FD1) sequence (SEQ ID NO: 163) and the FLRG_(ND)-FLRG_(FD1)-FLRG_(FD2) sequence (SEQ ID NO: 164), as set forth below, and, for example, one or more heterologous polypeptides. Moreover, it will be appreciated that any of the initial amino acids G or N, prior to the first cysteine may be removed by processing or intentionally eliminated without any consequence, and polypeptides comprising such slightly shorter polypeptides are further included.

If presented as FLRG-Fc, this indicates that an Fc domain is fused to the C-terminus of FLRG, which may or may not include an intervening linker. The Fc in this instance may be any immunoglobulin Fc portion as that term is defined herein. If presented as FLRG-G1Fc, this indicates that the Fc portion of IgG1 is fused at the C-terminus of FLRG. Unless indicated to the contrary, a protein described with this nomenclature will represent a human FLRG protein.

In certain embodiments, functional variants or modified forms of the follistatin polypeptides and FLRG polypeptides include fusion proteins having at least a portion of the follistatin polypeptide or FLRG polypeptide and one or more fusion domains, such as, for example, domains that facilitate isolation, detection, stabilization or multimerization of the polypeptide. Suitable fusion domains are discussed in detail above with reference to the ActRII polypeptides. In some embodiment, an antagonist agent of the disclosure is a fusion protein comprising an activin-binding portion of a follistatin polypeptide fused to an Fc domain. In another embodiment, an antagonist agent of the disclosure is a fusion protein comprising an activin binding portion of an FLRG polypeptide fused to an Fc domain.

9. WFIKKN1 and WFIKKN2

In addition to FSTN and FSTL3, two other genes have been identified whose protein products contain a follistatin domain motif and function as extracellular inhibitors of myostatin and GDF11. In humans, these closely related genes are named WFIKKN1 and WFIKKN2 based on their shared domain structure which includes a whey acidic protein domain, a follistatin-Kazal domain, an immunoglobulin domain, two tandem domains related to Kunitz-type protease inhibitor modules, and a netrin domain (Trexler et al (2001) Proc Natl Acad Sci USA 98:3705-3709; Trexler et al (2002) Biol Chem 383:223-228). WFIKKN2 is also known as WFIKKN-related protein (WFIKKNRP), and murine counterparts of these proteins are named GDF-associated serum protein-2 (Gasp2) and Gasp1, respectively, based on their ligand-binding ability (Hill et al (2003) Mol Endocrinol 17:1144-1154).

Native WFIKKN1 (GASP2) and WFIKKN2 (GASP1) proteins possess overlapping activity profiles that are nonetheless distinct from each other and from follistatin or FLRG. WFIKKNs bind with high affinity to myostatin, GDF11, and in some cases to myostatin propeptide, with binding to processed ligand mediated primarily by the follistatin domain (WFIKKN1_(FD), WFIKKN2_(FD)) and propeptide binding mediated primarily by the netrin domain (Hill et al., 2003; Kondas et al (2008) J Biol Chem 283:23677-23684). In contrast to follistatin and FLRG, neither WFIKKN1 nor WFIKKN2 bind activin (Szláma et al (2010) FEBS J 277:5040-5050). WFIKKN proteins inhibit myostatin and GDF11 signaling by blocking their access to activin type II receptors (Lee et al (2013) Proc Natl Acad Sci USA 110:E3713-E3722). Due to the presence of several protease inhibitory modules in both WFIKKNs, it is likely that they also regulate the action of multiple types of proteases. The tissue expression patterns of WFIKKN1 differ prenatally and postnatally from that of WFIKKN2, thus supporting the view that the two proteins serve distinct roles (Trexler et al (2002) Biol Chem 383:223-228).

Additional lines of evidence implicate WFIKKNs in the regulation of skeletal muscle mass. Mice with homozygous deletion of WFIKKN1 or WFIKKN2 display phenotypes consistent with overactivity of myostatin and GDF11, including a reduction in muscle weight, a shift in fiber type from fast glycolytic type IIb fibers to fast oxidative type IIa fibers, and impaired muscle regeneration (Lee et al (2013) Proc Natl Acad Sci USA 110:E3713-E3722). Conversely, broad overexpression of WFIKKN2 in mice leads mainly to a hypermuscular phenotype (Monestier et al (2012) BMC Genomics 13:541-551). Although both WFIKKN proteins bind to myostatin, WFIKKIN1 and WFIKKN2 may interact differently with myostatin propeptide and thus may differentially block the activation of ActRIIA or ActRIIB by semilatent myostatin, which is the native complex between myostatin and a single myostatin propeptide chain (Szláma et al (2013) FEBS J 280:3822-3839). Taken together, follistatin-related fusion proteins comprising a WFIKKN1 or WFIKKN2 polypeptide as disclosed herein would be predicted to help in treatment of alleviation of one or more symptoms related to kidney diseases (such as kidney tissue damage, fibrosis, and/or inflammation) in vivo without causing potentially undesirable effects associated with inhibition of endogenous activins.

The term “WFIKKN1 polypeptide” is used to refer to polypeptides comprising any naturally occurring polypeptide of WFIKKN1 as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. In certain preferred embodiments, WFIKKN1 polypeptides of the disclosure bind to and/or inhibit activity of myostatin, myostatin propeptide, complexes between myostatin and its propeptide, GDF11, and potentially activins (e.g., ligand-mediated activation of ActRIIA and/or ActRIIB Smad2/3 signaling). Variants of WFIKKN1 polypeptides that retain ligand binding properties can be identified using routine methods to assay interactions between WFIKKN1 and ligands (see, e.g., Kondas et al 2008; Szláma et al 2013). In addition, methods for making and testing libraries of polypeptides are described herein and such methods also pertain to making and testing variants of WFIKKN1.

For example, WFIKKN1 polypeptides include polypeptides comprising an amino acid sequence derived from the sequence of any known WFIKKN1 polypeptide having a sequence at least about 80% identical to the sequence of a WFIKKN1 polypeptide (for example, SEQ ID NOs: 165-167), and optionally at least 85%, 90%, 95%, 97%, 99% or greater identity to any of SEQ ID NOs: 165-167. The term “WFIKKN1 fusion polypeptide” may refer to fusion proteins that comprise any of the polypeptides mentioned above along with a heterologous (non-WFIKKN1) portion. An amino acid sequence is understood to be heterologous to WFIKKN1 if it is not uniquely found in human WFIKKN1, represented by SEQ ID NO: 165. Many examples of heterologous portions are provided herein, and such heterologous portions may be immediately adjacent, by amino acid sequence, to the WFIKKN1 polypeptide portion of a fusion protein, or separated by intervening amino acid sequence, such as a linker or other sequence.

The human WFIKKN1 precursor has the amino acid sequence of SEQ ID NO: 165 (NCBI Ref Seq NP_444514.1), with the signal peptide indicated by dotted underline and the follistatin domain (WFIKKN1_(FD)) indicated by solid underline.

Processed human WFIKKN1 has the amino acid sequence of SEQ ID NO: 166, with the follistatin domain indicated by solid underline. Moreover, it will be appreciated that any of the 13 amino acids prior to the first cysteine may be removed by processing or intentionally eliminated without substantial consequence, and polypeptides comprising such slightly smaller polypeptides are further included.

In certain aspects, the disclosure includes polypeptides comprising the WFIKKN1_(FD) domain as set forth below (SEQ ID NO: 167), and, for example, one or more heterologous polypeptides.

If presented as WFIKKN1-Fc, this indicates that an Fc portion is fused to the C-terminus of WFIKKN1, which may or may not include an intervening linker. The Fc in this instance may be any immunoglobulin Fc portion as that term is defined herein. If presented as WFIKKN1-G1Fc, this indicates that the Fc portion of IgG1 is fused at the C-terminus of WFIKKN1. Unless indicated to the contrary, a protein described with this nomenclature will represent a human WFIKKN1 protein.

The term “WFIKKN2 polypeptide” includes polypeptides comprising any naturally occurring polypeptide of WFIKKN2 as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity. In certain preferred embodiments, WFIKKN2 polypeptides of the disclosure bind to and/or inhibit activity of myostatin, myostatin propeptide, complexes between myostatin and its propeptide, GDF11, and potentially activins (e.g., ligand-mediated activation of ActRIIA and/or ActRIIB Smad2/3 signaling). Variants of WFIKKN2 polypeptides that retain ligand binding properties can be identified using routine methods to assay interactions between WFIKKN2 and ligands (see, e.g., Kondas et al (2008) J Biol Chem 283:23677-23684; Szláma et al (2013) FEBS J 280:3822-3839). In addition, methods for making and testing libraries of polypeptides are described herein and such methods also pertain to making and testing variants of WFIKKN2.

For example, WFIKKN2 polypeptides include polypeptides comprising an amino acid sequence derived from the sequence of any known WFIKKN2 polypeptide having a sequence at least about 80% identical to the sequence of a WFIKKN2 polypeptide (for example, SEQ ID NOs: 168-172), and optionally at least 85%, 90%, 95%, 97%, 99% or greater identity to any of SEQ ID NOs: 168-172. The term “WFIKKN2 fusion polypeptide” may refer to fusion proteins that comprise any of the polypeptides mentioned above along with a heterologous (non-WFIKKN2) portion. An amino acid sequence is understood to be heterologous to WFIKKN2 if it is not uniquely found in human WFIKKN2, represented by SEQ ID NO: 168. Many examples of heterologous portions are provided herein, and such heterologous portions may be immediately adjacent, by amino acid sequence, to the WFIKKN2 polypeptide portion of a fusion protein, or separated by intervening amino acid sequence, such as a linker or other sequence.

The human WFIKKN2 precursor has the amino acid sequence of SEQ ID NO: 168 (NCBI Ref Seq NP_783165.1), with the signal peptide indicated by dotted underline and the follistatin domain (WFIKKN2_(FD)) indicated by solid underline.

Processed human WFIKKN2 has the amino acid sequence of SEQ ID NO: 169, with the follistatin domain indicated by single underline. Moreover, it will be appreciated that any of the 11 amino acids prior to the first cysteine may be removed by processing or intentionally eliminated without substantial consequence, and polypeptides comprising such slightly smaller polypeptides are further included.

In certain aspects, the disclosure includes polypeptides comprising the WFIKKN2_(FD) domain as set forth in SEQ ID NO: 170, and, for example, one or more heterologous polypeptides.

The murine WFIKKN2 (GASP1) precursor has the following amino acid sequence of SEQ ID NO: 171 (NCBI Ref Seq NP_861540.2), with the signal peptide indicated by dotted underline and the follistatin domain (WFIKKN2_(FD)) indicated by solid underline.

Processed murine WFIKKN2 has the following amino acid sequence of SEQ ID NO: 172, with the follistatin domain indicated by single underline. Moreover, it will be appreciated that any of the 11 amino acids prior to the first cysteine may be removed by processing or intentionally eliminated without substantial consequence, and polypeptides comprising such slightly smaller polypeptides are further included.

If presented as WFIKKN2-Fc, this indicates that an Fc portion is fused to the C-terminus of WFIKKN2, which may or may not include an intervening linker. The Fc in this instance may be any immunoglobulin Fc portion as that term is defined herein. If presented as WFIKKN2-G1Fc, this indicates that the Fc portion of IgG1 is fused at the C-terminus of WFIKKN2. Unless indicated to the contrary, a protein described with this nomenclature will represent a human WFIKKN2 protein.

10. Lefty A and B

The Lefty A and B proteins are known to regulate Nodal and other proteins that signal through the ALK7 pathway. Accordingly, in other aspects, an ALK7 antagonist is a Lefty A or Lefty B polypeptide, which may be used alone or in combination with one or more additional supportive therapies and/or active agents as disclosed herein to achieve a desired effect (e.g., treat kidney disease and/or a metabolic condition or disorder).

The term “Lefty A polypeptide” includes polypeptides comprising any naturally occurring polypeptide of Lefty A as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity, and further includes any functional monomer or multimer of Lefty A. In certain preferred embodiments, Lefty A polypeptides of the disclosure bind to and/or inhibit nodal activity. In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII and ALK7 polypeptides, and such methods also pertain to making and testing variants of Lefty A. Lefty A polypeptides include polypeptides derived from the sequence of any known Lefty A having a sequence at least about 80% identical to the sequence of a Lefty A polypeptide, and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater identity. Examples of Lefty A polypeptides include the processed Lefty A polypeptide or shorter isoforms or other variants of the human Lefty A precursor polypeptide (SEQ ID NO: 173, the signal peptide is underlined; GenBank Id: AAD48145.1).

The term “Lefty B polypeptide” includes polypeptides comprising any naturally occurring polypeptide of Lefty B as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity, and further includes any functional monomer or multimer of Lefty B. In certain preferred embodiments, Lefty B polypeptides of the disclosure inhibit nodal activity. In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII and ALK7 polypeptides, and such methods also pertain to making and testing variants of Lefty B. Lefty B polypeptides include polypeptides derived from the sequence of any known Lefty B having a sequence at least about 80% identical to the sequence of a Lefty B polypeptide, and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater identity. Examples of Lefty B polypeptides include the processed Lefty B polypeptide or shorter isoforms or other variants of the human Lefty B precursor polypeptide (SEQ ID NO: 174, the signal peptide is underlined; GenBank Id: AAD48144.1).

In certain embodiments, functional variants or modified forms of the Lefty A polypeptides and Lefty B polypeptides include fusion proteins having at least a portion of the Lefty A polypeptide or Lefty polypeptide and one or more fusion domains, such as, for example, domains that facilitate isolation, detection, stabilization or multimerization of the polypeptide. Suitable fusion domains are discussed in detail above with reference to the ActRII and ALK7 polypeptides. In some embodiments, an antagonist agent of the disclosure is a fusion protein comprising a nodal-binding portion of a Lefty A and/or Lefty B polypeptide fused to an Fc domain.

11. DAN-Related Proteins

Members of the DAN family of proteins are known to regulate ligands that signal through the ALK7 pathway. Accordingly, in other aspects, an ALK7 antagonist is a DAN-related protein (e.g., Cerberus and Coco), which may be used alone or in combination with one or more additional supportive therapies and/or active agents as disclosed herein to achieve a desired effect (e.g., treat patients having kidney disease and/or a metabolic disorder).

The term “Cerberus polypeptide” includes polypeptides comprising any naturally occurring polypeptide of Cerberus as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity, and further includes any functional monomer or multimer of Cerberus. In certain preferred embodiments, Cerberus polypeptides of the disclosure bind to and/or inhibit nodal activity. In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII and ALK7 polypeptides, and such methods also pertain to making and testing variants of Cerberus. Cerberus polypeptides include polypeptides derived from the sequence of any known Cerberus having a sequence at least about 80% identical to the sequence of a Cerberus polypeptide, and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater identity. Examples of Cerberus polypeptides include the processed Cerberus polypeptide or shorter isoforms or other variants of the human Cerberus precursor polypeptide (SEQ ID NO: 175, the signal peptide is underlined; GenBank Id: NP_005445.1).

The term “Coco polypeptide,” also known as DAN domain BMP antagonist family member 5, SP1, CER2, CRL2, CERL2, DANTE, GREM3, and CKTSF1B3, includes polypeptides comprising any naturally occurring polypeptide of Coco as well as any variants thereof (including mutants, fragments, fusions, and peptidomimetic forms) that retain a useful activity, and further includes any functional monomer or multimer of Coco. In certain preferred embodiments, Coco polypeptides of the disclosure bind to and/or inhibit nodal activity. In addition, methods for making and testing libraries of polypeptides are described above in the context of ActRII and ALK7 polypeptides, and such methods also pertain to making and testing variants of Coco. Coco polypeptides include polypeptides derived from the sequence of any known Coco having a sequence at least about 80% identical to the sequence of a Coco polypeptide, and optionally at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or greater identity. Examples of Coco polypeptides include the processed Coco polypeptide or shorter isoforms or other variants of the human Coco precursor polypeptide (SEQ ID NO: 176, the signal peptide is underlined; GenBank Id: NP_689867.1).

In certain embodiments, functional variants or modified forms of the Cerberus polypeptides and Coco polypeptides include fusion proteins having at least a portion of the Cerberus polypeptide and/or Coco polypeptide and one or more fusion domains, such as, for example, domains that facilitate isolation, detection, stabilization or multimerization of the polypeptide. Suitable fusion domains are discussed in detail above with reference to the ActRII and ALK7 polypeptides. In some embodiments, an antagonist agent of the disclosure is a fusion protein comprising a nodal-binding portion of a Cerberus and/or Coco polypeptide fused to an Fc domain.

12. Screening Assays

In certain aspects, the present disclosure relates to the use of the subject activin and/or GDF antagonists (e.g., inhibitors, or combinations of inhibitors, of one or more of: activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad3) to identify compounds (agents) which may be used to treat or reduce the progression rate, frequency, and/or severity of kidney diseases, particularly treating, preventing, or reducing the progression rate, frequency, and/or severity of one or more kidney-disease-associated complications (e.g., kidney tissue damage, fibrosis, and/or inflammation).

There are numerous approaches to screening for therapeutic agents for treating kidney diseases by targeting signaling (e.g., Smad signaling) of one or more GDF ligands. In certain embodiments, high-throughput screening of compounds can be carried out to identify agents that perturb GDF ligand-mediated effects on a selected cell line. In certain embodiments, the assay is carried out to screen and identify compounds that specifically inhibit or reduce binding of a GDF ligand (e.g., activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, etc.) to its binding partner, such as a type II receptor (e.g., ActRIIA and/or ActRIIB), a co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), or a type I receptor (e.g., ALK4, ALK5, and/or ALK7). Alternatively, the assay can be used to identify compounds that enhance binding of a GDF ligand to its binding partner such as a type II receptor. In a further embodiment, the compounds can be identified by their ability to interact with a type II receptor.

A variety of assay formats will suffice and, in light of the present disclosure, those not expressly described herein will nevertheless be comprehended by one of ordinary skill in the art. As described herein, the test compounds (agents) of the invention may be created by any combinatorial chemical method. Alternatively, the subject compounds may be naturally occurring biomolecules synthesized in vivo or in vitro. Compounds (agents) to be tested for their ability to act as modulators of tissue growth can be produced, for example, by bacteria, yeast, plants or other organisms (e.g., natural products), produced chemically (e.g., small molecules, including peptidomimetics), or produced recombinantly. Test compounds contemplated by the present invention include non-peptidyl organic molecules, peptides, polypeptides, peptidomimetics, sugars, hormones, and nucleic acid molecules. In certain embodiments, the test agent is a small organic molecule having a molecular weight of less than about 2,000 Daltons.

The test compounds of the disclosure can be provided as single, discrete entities, or provided in libraries of greater complexity, such as made by combinatorial chemistry. These libraries can comprise, for example, alcohols, alkyl halides, amines, amides, esters, aldehydes, ethers and other classes of organic compounds. Presentation of test compounds to the test system can be in either an isolated form or as mixtures of compounds, especially in initial screening steps. Optionally, the compounds may be optionally derivatized with other compounds and have derivatizing groups that facilitate isolation of the compounds. Non-limiting examples of derivatizing groups include biotin, fluorescein, digoxygenin, green fluorescent protein, isotopes, polyhistidine, magnetic beads, glutathione S-transferase (GST), photoactivatible crosslinkers or any combinations thereof.

In many drug-screening programs which test libraries of compounds and natural extracts, high-throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays which are performed in cell-free systems, such as may be derived with purified or semi-purified proteins, are often preferred as “primary” screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target induced by a test compound. Moreover, the effects of cellular toxicity or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity between a GDF ligand (e.g., activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, etc.) and its binding partner, such as an a type II receptor (e.g., ActRIIA and/or ActRIIB), a co-receptor (e.g., Cripto, Cryptic, and/or Cryptic 1B), or a type I receptor (e.g., ALK4, ALK5, and/or ALK7).

Merely to illustrate, in an exemplary screening assay of the present disclosure, the compound of interest is contacted with an isolated and purified ActRIIB polypeptide which is ordinarily capable of binding to an ActRIIB ligand, as appropriate for the intention of the assay. To the mixture of the compound and ActRIIB polypeptide is then added to a composition containing an ActRIIB ligand (e.g., GDF11). Detection and quantification of ActRIIB/ActRIIB-ligand complexes provides a means for determining the compound's efficacy at inhibiting (or potentiating) complex formation between the ActRIIB polypeptide and its binding protein. The efficacy of the compound can be assessed by generating dose-response curves from data obtained using various concentrations of the test compound. Moreover, a control assay can also be performed to provide a baseline for comparison. For example, in a control assay, isolated and purified ActRIIB ligand is added to a composition containing the ActRIIB polypeptide, and the formation of ActRIIB/ActRIIB ligand complex is quantitated in the absence of the test compound. It will be understood that, in general, the order in which the reactants may be admixed can be varied, and can be admixed simultaneously. Moreover, in place of purified proteins, cellular extracts and lysates may be used to render a suitable cell-free assay system.

Complex formation between GDF ligand and its binding protein may be detected by a variety of techniques. For instance, modulation of the formation of complexes can be quantitated using, for example, detectably labeled proteins such as radiolabeled (e.g., ³²P, ³⁵S, ¹⁴C, or ³H), fluorescently labeled (e.g., FITC), or enzymatically labeled ActRIIB polypeptide and/or its binding protein, by immunoassay, or by chromatographic detection.

In certain embodiments, the present disclosure contemplates the use of fluorescence polarization assays and fluorescence resonance energy transfer (FRET) assays in measuring, either directly or indirectly, the degree of interaction between a GDF ligand and its binding protein. Further, other modes of detection, such as those based on optical waveguides (see, e.g., PCT Publication WO 96/26432 and U.S. Pat. No. 5,677,196), surface plasmon resonance (SPR), surface charge sensors, and surface force sensors, are compatible with many embodiments of the disclosure.

Moreover, the present disclosure contemplates the use of an interaction trap assay, also known as the “two-hybrid assay,” for identifying agents that disrupt or potentiate interaction between a GDF ligand and its binding partner. See, e.g., U.S. Pat. No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J Biol Chem 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; and Iwabuchi et al. (1993) Oncogene 8:1693-1696). In a certain embodiments, the present disclosure contemplates the use of reverse two-hybrid systems to identify compounds (e.g., small molecules or peptides) that dissociate interactions between a GDF ligand and its binding protein (see, e.g., Vidal and Legrain, (1999) Nucleic Acids Res 27:919-29; Vidal and Legrain, (1999) Trends Biotechnol 17:374-81; and U.S. Pat. Nos. 5,525,490; 5,955,280; and 5,965,368).

In certain embodiments, the subject compounds are identified by their ability to interact with a GDF ligand. The interaction between the compound and the GDF ligand may be covalent or non-covalent. For example, such interaction can be identified at the protein level using in vitro biochemical methods, including photo-crosslinking, radiolabeled ligand binding, and affinity chromatography (see, e.g., Jakoby W B et al. (1974) Methods in Enzymology 46:1). In certain cases, the compounds may be screened in a mechanism-based assay, such as an assay to detect compounds which bind to a GDFP ligand. This may include a solid-phase or fluid-phase binding event. Alternatively, the gene encoding GDF ligand can be transfected with a reporter system (e.g., β-galactosidase, luciferase, or green fluorescent protein) into a cell and screened against the library preferably by high-throughput screening or with individual members of the library. Other mechanism-based binding assays may be used; for example, binding assays which detect changes in free energy. Binding assays can be performed with the target fixed to a well, bead or chip or captured by an immobilized antibody or resolved by capillary electrophoresis. The bound compounds may be detected usually using colorimetric endpoints or fluorescence or surface plasmon resonance.

13. Therapeutic Uses

In part, the present disclosure relates to methods of treating kidney disease comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist (e.g., an antagonist of one or more of activin (e.g., activin A, activin B, activin AB, activin C, activin AC, activin BC, activin E, activin AE, and/or activin BE), GDF8, GDF11, GDF3, GDF1, Nodal, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cryptic, Cryptic 1B, Smad 2, and Smad 3). In some embodiments, the disclosure contemplates methods of treating one or more complications of a kidney disease (e.g., any kidney disease-related symptoms, such as tissue damage, fibrosis, and/or inflammation) comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of preventing one or more complications of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the progression rate of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the progression rate of one or more complications of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the frequency of kidney-disease-related disease events, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the frequency of one or more complications of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the severity of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. In some embodiments, the disclosure contemplates methods of reducing the severity of one or more complications of a kidney disease, comprising administering to a patient in need thereof an effective amount of an activin and/or GDF antagonist. Optionally, methods disclosed herein for treating or reducing the progression rate, frequency, and/or severity of a kidney disease and kidney-disease-related disease events, particularly treating, preventing, or reducing the progression rate, frequency, and/or severity of one or more complications of a kidney disease, may further comprise administering to the patient one or more supportive therapies or additional active agents for treating a kidney disease. For example, the patient also may be administered one or more supportive therapies or active agents to treat or alleviate one or more symptoms, such as high blood pressure (e.g., using angiotensin-converting enzyme (ACE) inhibitors or angiotensin II receptor blockers or a water pill (diuretic), optionally with a low-salt diet), high cholesterol levels (e.g., using statins), anemia (e.g., using hormone erythropoietin, optionally with iron supplement), swelling (e.g., using diuretics), lack of fluids in blood (e.g., with intravenous (IV) fluid supplement), lack of calcium or bone failure (e.g, with calcium and/or vitamin D supplement, or a phosphate binder to lower the blood phosphate level and to protect calcification of blood vessels), high blood potassium level (e.g., using calcium, glucose or sodium polystyrene sulfonate (Kayexalate, Kionex) to lower potassium levels), toxin accumulation (e.g., by hemodialysis and/or peritoneal dialysis), etc. In addition, kidney transplant may be also used as an additional therapy. Some exemplary medications for kidney diseases are Lasix® (furosemide), Demadex® (torsemide), Edecrin® (ethacrynic acid), and sodium edecrin.

As used herein, a therapeutic that “prevents” a disorder or condition refers to a compound that, in a statistical sample, reduces the occurrence of the disorder or condition in the treated sample relative to an untreated control sample, delays the onset or reduces the frequency of disorder-related events, or reduces the severity of one or more symptoms of the disorder or condition relative to the untreated control sample.

The term “treating” as used herein includes amelioration or elimination of the condition once it has been established. In either case, prevention or treatment may be discerned in the diagnosis provided by a physician or other health care provider and the intended result of administration of the therapeutic agent.

In general, treatment or prevention of a disease or condition as described in the present disclosure is achieved by administering an activin and/or GDF antagonist in an effective amount. An effective amount of an agent refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. A therapeutically effective amount of an agent of the present disclosure may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the agent to elicit a desired response in the individual. A prophylactically effective amount refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result.

The terms “subject,” an “individual,” or a “patient” are interchangeable throughout the specification and generally refer to mammals. Mammals include, but are not limited to, domesticated animals (e.g., cows, sheep, cats, dogs, and horses), primates (e.g., humans and non-human primates such as monkeys), rabbits, and rodents (e.g., mice and rats).

In general, treatment or prevention of a kidney-related disease or condition as described in the present disclosure is achieved by administering an activin and/or GDF antagonist, or combinations of such antagonists, of the present disclosure in an “effective amount”. An effective amount of an agent refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. A “therapeutically effective amount” of an agent of the present disclosure may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the agent to elicit a desired response in the individual. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result.

The kidneys maintain many features of the blood, including volume, pH balance, electrolyte concentrations, and blood pressure, as well as bearing responsibility for toxin and waste filtration. These functions depend upon the intricate structure of the kidney nephrons, constant flow of blood through the various capillaries of the kidney, and the regulation of the kidney by signals from the rest of the body, including endocrine hormones. Problems with kidney function manifest by direct mechanisms (e.g., genetic defects, infection, or toxin exposure) and by indirect mechanisms progressively proceeding from long term stressors like hypertrophy and hyperfiltration (themselves often a result of more direct insults to kidney function). Due to the central role of the kidney in blood maintenance and waste secretion, kidney-associated disease manifestations are many and varied; they can be reviewed in Harrison's Principles of Internal Medicine, 18^(th) edition, McGraw Hill, N.Y., Part 13, Chp 277-289.

As described herein, an activin and/or GDF antagonist had various beneficial effects in a kidney disease model. In particular, treatment with an ALK7:ActRIIB heteromultimer reduced kidney tissue damage, inflammation, and fibrosis in subjects having unilateral ureteral obstruction (UUO). These data indicate that an activin and/or GDF antagonist may be used to treat or prevent kidney disease, particularly treating or preventing various complications (manifestations) of kidney disease including, for example, kidney tissue damage, inflammation, and/or fibrosis.

Therefore, methods of this invention can be applied to various kidney-associated diseases or conditions. As used herein, “kidney-associated disease or condition” can refer to any disease, disorder, or condition that affects the kidneys or the renal system. Examples of kidney-associated diseases or conditions include, but are not limited to, chronic kidney diseases (or failure), acute kidney diseases (or failure), primary kidney diseases, non-diabetic kidney diseases, glomerulonephritis, interstitial nephritis, diabetic kidney diseases, diabetic chronic kidney disease, diabetic nephropathy, glomerulosclerosis, rapid progressive glomerulonephritis, renal fibrosis, Alport syndrome, IDDM nephritis, mesangial proliferative glomerulonephritis, membranoproliferative glomerulonephritis, crescentic glomerulonephritis, renal interstitial fibrosis, focal segmental glomerulosclerosis, membranous nephropathy, minimal change disease, pauci-immune rapid progressive glomerulonephritis, IgA nephropathy, polycystic kidney disease, Dent's disease, nephrocytinosis, Heymann nephritis, polycystic kidney disease (e.g., autosomal dominant (adult) polycystic kidney disease and autosomal recessive (childhood) polycystic kidney disease), acute kidney injury, nephrotic syndrome, renal ischemia, podocyte diseases or disorders, proteinuria, glomerular diseases, membranous glomerulonephritis, focal segmental glomerulonephritis, pre-eclampsia, eclampsia, kidney lesions, collagen vascular diseases, benign orthostatic (postural) proteinuria, IgM nephropathy, membranous nephropathy, sarcoidosis, diabetes mellitus, kidney damage due to drugs, Fabry's disease, aminoaciduria, Fanconi syndrome, hypertensive nephrosclerosis, interstitial nephritis, acute interstitial nephritis, Sickle cell disease, hemoglobinuria, myoglobinuria, Wegener's Granulomatosis, Glycogen Storage Disease Type 1, chronic kidney disease, chronic renal failure, low Glomerular Filtration Rate (GFR), nephroangiosclerosis, lupus nephritis, ANCA-positive pauci-immune crescentic glomerulonephritis, chronic allograft nephropathy, nephrotoxicity, renal toxicity, kidney necrosis, kidney damage, glomerular and tubular injury, kidney dysfunction, nephritic syndrome, acute renal failure, chronic renal failure, proximal tubal dysfunction, acute kidney transplant rejection, chronic kidney transplant rejection, non-IgA mesangioproliferative glomerulonephritis, postinfectious glomerulonephritis, vasculitides with renal involvement of any kind, any hereditary renal disease, any interstitial nephritis, renal transplant failure, kidney cancer, kidney disease associated with other conditions (e.g., hypertension, diabetes, and autoimmune disease), Dent's disease, nephrocytinosis, Heymann nephritis, a primary kidney disease, a collapsing glomerulopathy, a dense deposit disease, a cryoglobulinemia-associated glomerulonephritis, an Henoch-Schonlein disease, a postinfectious glomerulonephritis, a bacterial endocarditis, a microscopic polyangitis, a Churg-Strauss syndrome, an anti-GBM-antibody mediated glomerulonephritis, amyloidosis, a monoclonal immunoglobulin deposition disease, a fibrillary glomerulonephritis, an immunotactoid glomerulopathy, ischemic tubular injury, a medication-induced tubulo-interstitial nephritis, a toxic tubulo-interstitial nephritis, an infectious tubulo-interstitial nephritis, a bacterial pyelonephritis, a viral infectious tubulo-interstitial nephritis which results from a polyomavirus infection or an HIV infection, a metabolic-induced tubulo-interstitial disease, a mixed connective disease, a cast nephropathy, a crystal nephropathy which may results from urate or oxalate or drug-induced crystal deposition, an acute cellular tubulo-interstitial allograft rejection, a tumoral infiltrative disease which results from a lymphoma or a post-transplant lymphoproliferative disease, an obstructive disease of the kidney, vascular disease, a thrombotic microangiopathy, a nephroangiosclerosis, an atheroembolic disease, a mixed connective tissue disease, a polyarteritis nodosa, a calcineurin-inhibitor induced-vascular disease, an acute cellular vascular allograft rejection, an acute humoral allograft rejection, early renal function decline (ERFD), end stage renal disease (ESRD), renal vein thrombosis, acute tubular necrosis, acute interstitial nephritis, established chronic kidney disease, renal artery stenosis, ischemic nephropathy, uremia, drug and toxin-induced chronic tubulointerstitial nephritis, reflux nephropathy, kidney stones, Goodpasture's syndrome, normocytic normochromic anemia, renal anemia, diabetic chronic kidney disease, IgG4-related disease, von Hippel-Lindau syndrome, tuberous sclerosis, nephronophthisis, medullary cystic kidney disease, renal cell carcinoma, adenocarcinoma, nephroblastoma, lymphoma, leukemia, hyposialylation disorder, chronic cyclosporine nephropathy, renal reperfusion injury, renal dysplasia, azotemia, bilateral arterial occlusion, acute uric acid nephropathy, hypovolemia, acute bilateral obstructive uropathy, hypercalcemic nephropathy, hemolytic uremic syndrome, acute urinary retention, malignant nephrosclerosis, postpartum glomerulosclerosis, scleroderma, non-Goodpasture's anti-GBM disease, microscopic polyarteritis nodosa, allergic granulomatosis, acute radiation nephritis, post-streptococcal glomerulonephritis, Waldenstrom's macroglobulinemia, analgesic nephropathy, arteriovenous fistula, arteriovenous graft, dialysis, ectopic kidney, medullary sponge kidney, renal osteodystrophy, solitary kidney, hydronephrosis, microalbuminuria, uremia, haematuria, hyperlipidemia, hypoalbuminaemia, lipiduria, acidosis, edma, tubulointerstitial renal fibrosis, hypertensive sclerosis, juxtaglomerular cell tumor, Fraser syndrome, Horseshoe kidney, renal tubular dysgenesis, hypokalemia, hypomagnesemia, hypercalcemia, hypophosphatemia, uromodulin-associated kidney disease, Nail-patella syndrome, lithium nephrotoxity, TNF-alpha nephrotoxicity, honeybee resin related renal failure, sugarcane harvesting acute renal failure, complete LCAT deficiency, Fraley syndrome, Page kidney, reflux nephropathy, Bardet-Biedl syndrome, collagenofibrotic glomerulopathy, Dent disease, Denys-Drash syndrome, congenital nephrotic syndrome, immunotactoid glomerulopathy, fibronextin glomerulopathy, Galloway Mowat syndrome, lipoprotein glomerulopathy, MesoAmerican nephropathy, beta-thalassemia renal disease, haemolytic uraemic syndrome, Henoch-Schonlein-Purpura disease, retroperitoneal fibrosis, polyarteritis nodose, cardiorenal syndrome, medullary kidney disease, renal artery stenosis, uromodulin kidney disease, and hyperkalemia.

In some embodiments, an activin and/or GDF antagonist, or combinations of such antagonists, of the present disclosure may be used to treat or prevent chronic kidney disease, optionally in combination with one or more supportive therapies for treating chronic kidney disease. In some embodiments, an activin and/or GDF antagonist, or combinations of such antagonists, of the present disclosure may be used to treat or prevent one or more complications (symptoms or manifestations) of chronic kidney disease (e.g., tissue damage, inflammation, and/or fibrosis), optionally in combination with one or more supportive therapies for treating chronic kidney disease. In some embodiments, an activin and/or GDF antagonist, or combinations of such antagonists, of the present disclosure may be used to treat or prevent end-stage kidney failure, optionally in combination with one or more supportive therapies for treating end-stage kidney disease. Chronic kidney disease (CKD), also known as chronic renal disease, is a progressive loss in renal function over a period of months or years. The symptoms of worsening kidney function may include feeling generally unwell and experiencing a reduced appetite. Often, chronic kidney disease is diagnosed as a result of screening of people known to be at risk of kidney problems, such as those with high blood pressure or diabetes and those with a blood relative with CKD. This disease may also be identified when it leads to one of its recognized complications, such as cardiovascular disease, anemia, or pericarditis. Recent professional guidelines classify the severity of CKD in five stages, with stage 1 being the mildest and usually causing few symptoms and stage 5 being a severe illness with poor life expectancy if untreated. Stage 5 CKD is often called end-stage kidney disease, end-stage renal disease, or end-stage kidney failure, and is largely synonymous with the now outdated terms chronic renal failure or chronic kidney failure; and usually means the patient requires renal replacement therapy, which may involve a form of dialysis, but ideally constitutes a kidney transplant. CKD is initially without specific symptoms and is generally only detected as an increase in serum creatinine or protein in the urine. As the kidney function decreases, various symptoms may manifest as described below. Blood pressure may be increased due to fluid overload and production of vasoactive hormones created by the kidney via the renin-angiotensin system, increasing one's risk of developing hypertension and/or suffering from congestive heart failure. Urea may accumulate, leading to azotemia and ultimately uremia (symptoms ranging from lethargy to pericarditis and encephalopathy). Due to its high systemic circulation, urea is excreted in eccrine sweat at high concentrations and crystallizes on skin as the sweat evaporates (“uremic frost”). Potassium may accumulate in the blood (hyperkalemia with a range of symptoms including malaise and potentially fatal cardiac arrhythmias). Hyperkalemia usually does not develop until the glomerular filtration rate falls to less than 20-25 ml/min/1.73 m², at which point the kidneys have decreased ability to excrete potassium. Hyperkalemia in CKD can be exacerbated by acidemia (which leads to extracellular shift of potassium) and from lack of insulin. Erythropoietin synthesis may be decreased causing anemia. Fluid volume overload symptoms may occur, ranging from mild edema to life-threatening pulmonary edema. Hyperphosphatemia, due to reduced phosphate excretion, may occur generally following the decrease in glomerular filtration. Hyperphosphatemia is associated with increased cardiovascular risk, being a direct stimulus to vascular calcification. Hypocalcemia may manifest, which is generally caused by stimulation of fibroblast growth factor-23. Osteocytes are responsible for the increased production of FGF23, which is a potent inhibitor of the enzyme 1-alpha-hydroxylase (responsible for the conversion of 25-hydroxycholecalciferol into 1,25-dihydroxyvitamin D3). Later, this progresses to secondary hyperparathyroidism, renal osteodystrophy, and vascular calcification that further impairs cardiac function. Metabolic acidosis (due to accumulation of sulfates, phosphates, uric acid etc.) may occur and cause altered enzyme activity by excess acid acting on enzymes; and also increased excitability of cardiac and neuronal membranes by the promotion of hyperkalemia due to excess acid (acidemia). Acidosis is also due to decreased capacity to generate enough ammonia from the cells of the proximal tubule. Iron deficiency anemia, which increases in prevalence as kidney function decreases, is especially prevalent in those requiring haemodialysis. It is multifactoral in cause, but includes increased inflammation, reduction in erythropoietin, and hyperuricemia leading to bone marrow suppression. People with CKD suffer from accelerated atherosclerosis and are more likely to develop cardiovascular disease than the general population. Patients afflicted with CKD and cardiovascular disease tend to have significantly worse prognoses than those suffering only from the latter.

In another embodiment, an activin and/or GDF antagonist, or combinations of such antagonists, may be used in patients with chronic kidney disease mineral bone disorder (CKD-MBD), a broad syndrome of interrelated skeletal, cardiovascular, and mineral-metabolic disorders arising from kidney disease. CKD-MBD encompasses various skeletal pathologies often referred to as renal osteodystrophy (ROD), which is a preferred embodiment for treatment with, an activin and/or GDF antagonist, or combinations of such antagonists. Depending on the relative contribution of different pathogenic factors, ROD is manifested as diverse pathologic patterns of bone remodeling (Hruska et al., 2008, Chronic kidney disease mineral bone disorder (CKD-MBD); in Rosen et al. (ed) Primer on the Metabolic Bone Diseases and Disorders of Mineral Metabolism, 7th ed. American Society for Bone and Mineral Research, Washington D.C., pp 343-349). At one end of the spectrum is ROD with uremic osteodystrophy and low bone turnover, characterized by a low number of active remodeling sites, profoundly suppressed bone formation, and low bone resorption. At the other extreme is ROD with hyperparathyroidism, high bone turnover, and osteitis fibrosa. Given that an activin and/or GDF antagonist, or combinations of such antagonists, may exert both anabolic and antiresorptive effects, these agents may be useful in patients across the ROD pathology spectrum.

In certain embodiments, the present disclosure provides methods for managing a patient that has been treated with, or is a candidate to be treated with, one or more one or more activin and/or GDF antagonists of the disclosure by measuring one or more hematologic parameters in the patient. The hematologic parameters may be used to evaluate appropriate dosing for a patient who is a candidate to be treated with the antagonist of the present disclosure, to monitor the hematologic parameters during treatment, to evaluate whether to adjust the dosage during treatment with one or more antagonist of the disclosure, and/or to evaluate an appropriate maintenance dose of one or more antagonists of the disclosure. If one or more of the hematologic parameters are outside the normal level, dosing with one or more activin and/or GDF antagonists may be reduced, delayed or terminated.

Hematologic parameters that may be measured in accordance with the methods provided herein include, for example, red blood cell levels, blood pressure, iron stores, and other agents found in bodily fluids that correlate with increased red blood cell levels, using art-recognized methods. Such parameters may be determined using a blood sample from a patient. Increases in red blood cell levels, hemoglobin levels, and/or hematocrit levels may cause increases in blood pressure.

In one embodiment, if one or more hematologic parameters are outside the normal range or on the high side of normal in a patient who is a candidate to be treated with one or more activin and/or GDF antagonists, then onset of administration of the one or more activin and/or GDF antagonists of the disclosure may be delayed until the hematologic parameters have returned to a normal or acceptable level either naturally or via therapeutic intervention. For example, if a candidate patient is hypertensive or pre-hypertensive, then the patient may be treated with a blood-pressure-lowering agent in order to reduce the patient's blood pressure. Any blood-pressure-lowering agent appropriate for the individual patient's condition may be used including, for example, diuretics, adrenergic inhibitors (including alpha blockers and beta blockers), vasodilators, calcium channel blockers, angiotensin-converting enzyme (ACE) inhibitors, or angiotensin II receptor blockers. Blood pressure may alternatively be treated using a diet and exercise regimen. Similarly, if a candidate patient has iron stores that are lower than normal, or on the low side of normal, then the patient may be treated with an appropriate regimen of diet and/or iron supplements until the patient's iron stores have returned to a normal or acceptable level. For patients having higher than normal red blood cell levels and/or hemoglobin levels, then administration of the one or more antagonists of the disclosure may be delayed until the levels have returned to a normal or acceptable level.

In certain embodiments, if one or more hematologic parameters are outside the normal range or on the high side of normal in a patient who is a candidate to be treated with one or more activin and/or GDF antagonists, then the onset of administration may not be delayed. However, the dosage amount or frequency of dosing of the one or more activin and/or GDF antagonists of the disclosure may be set at an amount that would reduce the risk of an unacceptable increase in the hematologic parameters arising upon administration of the one or more activin and/or GDF antagonists of the disclosure. Alternatively, a therapeutic regimen may be developed for the patient that combines one or more activin and/or GDF antagonists with a therapeutic agent that addresses the undesirable level of the hematologic parameter. For example, if the patient has elevated blood pressure, then a therapeutic regimen may be designed involving administration of one or more activin and/or GDF antagonist agents and a blood-pressure-lowering agent. For a patient having lower than desired iron stores, a therapeutic regimen may be developed involving one or more activin and/or GDF antagonists of the disclosure and iron supplementation.

In one embodiment, baseline parameter(s) for one or more hematologic parameters may be established for a patient who is a candidate to be treated with one or more activin and/or GDF antagonists of the disclosure and an appropriate dosing regimen established for that patient based on the baseline value(s). Alternatively, established baseline parameters based on a patient's medical history could be used to inform an appropriate activin and/or GDF antagonist dosing regimen for a patient. For example, if a healthy patient has an established baseline blood pressure reading that is above the defined normal range it may not be necessary to bring the patient's blood pressure into the range that is considered normal for the general population prior to treatment with the one or more antagonist of the disclosure. A patient's baseline values for one or more hematologic parameters prior to treatment with one or more activin and/or GDF antagonists of the disclosure may also be used as the relevant comparative values for monitoring any changes to the hematologic parameters during treatment with the one or more activin and/or GDF antagonists of the disclosure.

In certain embodiments, one or more hematologic parameters are measured in patients who are being treated with one or more activin and/or GDF antagonists. The hematologic parameters may be used to monitor the patient during treatment and permit adjustment or termination of the dosing with the one or more activin and/or GDF antagonists of the disclosure or additional dosing with another therapeutic agent. For example, if administration of one or more activin and/or GDF antagonists results in an increase in blood pressure, red blood cell level, or hemoglobin level, or a reduction in iron stores, then the dose of the one or more antagonists of the disclosure may be reduced in amount or frequency in order to decrease the effects of the one or more activin and/or GDF antagonists of the disclosure on the one or more hematologic parameters. If administration of one or more activin and/or GDF antagonists results in a change in one or more hematologic parameters that is adverse to the patient, then the dosing of the one or more activin and/or GDF antagonists of the disclosure may be terminated either temporarily, until the hematologic parameter(s) return to an acceptable level, or permanently. Similarly, if one or more hematologic parameters are not brought within an acceptable range after reducing the dose or frequency of administration of the one or more activin and/or GDF antagonists of the disclosure, then the dosing may be terminated. As an alternative, or in addition, to reducing or terminating the dosing with the one or more activin and/or GDF antagonists of the disclosure, the patient may be dosed with an additional therapeutic agent that addresses the undesirable level in the hematologic parameter(s), such as, for example, a blood-pressure-lowering agent or an iron supplement. For example, if a patient being treated with one or more activin and/or GDF antagonists has elevated blood pressure, then dosing with the one or more activin and/or GDF antagonists of the disclosure may continue at the same level and a blood-pressure-lowering agent is added to the treatment regimen, dosing with the one or more activin and/or GDF antagonist of the disclosure may be reduced (e.g., in amount and/or frequency) and a blood-pressure-lowering agent is added to the treatment regimen, or dosing with the one or more activin and/or GDF antagonist of the disclosure may be terminated and the patient may be treated with a blood-pressure-lowering agent.

14. Pharmaceutical Compositions

The therapeutic agents described herein (e.g., activin and/or GDF antagonists) may be formulated into pharmaceutical compositions. Pharmaceutical compositions for use in accordance with the present disclosure may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.

In certain embodiments, the therapeutic methods of the disclosure include administering the composition systemically, or locally as an implant or device. When administered, the therapeutic composition for use in this disclosure may be in any physiologically acceptable form, such as in a substantially pyrogen-free, or pyrogen-free, physiologically acceptable form. Therapeutically useful agents other than the activin and/or GDF antagonists, which may also optionally be included in the composition as described above, may be administered simultaneously or sequentially with the subject compounds in the methods disclosed herein.

Typically, protein therapeutic agents disclosed herein will be administered parenterally, and particularly intravenously or subcutaneously. Pharmaceutical compositions suitable for parenteral administration may comprise one or more activin and/or GDF antagonists in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents. Examples of suitable aqueous and nonaqueous carriers which may be employed in the pharmaceutical compositions of the disclosure include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

The compositions and formulations may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration

Further, the composition may be encapsulated or injected in a form for delivery to a target tissue site. In certain embodiments, compositions of the present invention may include a matrix capable of delivering one or more therapeutic compounds (e.g., activin and/or GDF antagonists) to a target tissue site, providing a structure for the developing tissue and optimally capable of being resorbed into the body. For example, the matrix may provide slow release of the activin and/or GDF antagonist. Such matrices may be formed of materials presently in use for other implanted medical applications.

The choice of matrix material is based on biocompatibility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the subject compositions will define the appropriate formulation. Potential matrices for the compositions may be biodegradable and chemically defined calcium sulfate, tricalcium phosphate, hydroxyapatite, polylactic acid and polyanhydrides. Other potential materials are biodegradable and biologically well defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are non-biodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability.

In certain embodiments, methods of the invention can be administered for orally, e.g., in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of an agent as an active ingredient. An agent may also be administered as a bolus, electuary or paste.

In certain embodiments, the methods of the invention may be formulated for intranasal administration. Nasal administration of the present invention may comprise the use of a nasal spray which uses water or salt solutions as the liquid carrier with one or more therapeutic compounds (e.g., activin and/or GDF antagonists) being dispersed or dissolved in the water in a therapeutically effective amount.

In solid dosage forms for oral administration (capsules, tablets, pills, dragees, powders, granules, and the like), one or more therapeutic compounds of the present invention may be mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose, and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and (10) coloring agents. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.

Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming, and preservative agents.

Suspensions, in addition to the active compounds, may contain suspending agents such as ethoxylated isostearyl alcohols, polyoxyethylene sorbitol, and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

The compositions of the invention may also contain adjuvants, such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption, such as aluminum monostearate and gelatin.

It is understood that the dosage regimen will be determined by the attending physician considering various factors which modify the action of the subject compounds of the disclosure (e.g., activin and/or GDF antagonists). The various factors include, but are not limited to, the patient's age, sex, and diet, the severity of the disease, time of administration, and other clinical factors. Optionally, the dosage may vary with the type of matrix used in the reconstitution and the types of compounds in the composition. The addition of other known growth factors to the final composition, may also affect the dosage. Progress can be monitored by periodic assessment of the ESS or hematologic parameters.

In certain embodiments, the present invention also provides gene therapy for the in vivo production of activin and/or GDF antagonists. Such therapy would achieve its therapeutic effect by introduction of the activin and/or GDF antagonist polynucleotide sequences into cells or tissues having the disorders as listed above. Delivery of activin and/or GDF antagonist polynucleotide sequences can be achieved using a recombinant expression vector such as a chimeric virus or a colloidal dispersion system. Preferred for therapeutic delivery of activin and/or GDF antagonist polynucleotide sequences is the use of targeted liposomes.

Various viral vectors which can be utilized for gene therapy as taught herein include adenovirus, herpes virus, vaccinia, or, preferably, an RNA virus such as a retrovirus. Preferably, the retroviral vector is a derivative of a murine or avian retrovirus. Examples of retroviral vectors in which a single foreign gene can be inserted include, but are not limited to: Moloney murine leukemia virus (MoMuLV), Harvey murine sarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV), and Rous Sarcoma Virus (RSV). A number of additional retroviral vectors can incorporate multiple genes. All of these vectors can transfer or incorporate a gene for a selectable marker so that transduced cells can be identified and generated. Retroviral vectors can be made target-specific by attaching, for example, a sugar, a glycolipid, or a protein. Preferred targeting is accomplished by using an antibody. Those of skill in the art will recognize that specific polynucleotide sequences can be inserted into the retroviral genome or attached to a viral envelope to allow target specific delivery of the retroviral vector containing the activin and/or GDF antagonist. In a preferred embodiment, the vector is targeted to bone or cartilage.

Alternatively, tissue culture cells can be directly transfected with plasmids encoding the retroviral structural genes gag, pol and env, by conventional calcium phosphate transfection. These cells are then transfected with the vector plasmid containing the genes of interest. The resulting cells release the retroviral vector into the culture medium.

Another targeted delivery system for activin and/or GDF antagonist polynucleotides is a colloidal dispersion system. Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. The preferred colloidal system of this invention is a liposome. Liposomes are artificial membrane vesicles which are useful as delivery vehicles in vitro and in vivo. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (see e.g., Fraley, et al., Trends Biochem. Sci., 6:77, 1981). Methods for efficient gene transfer using a liposome vehicle, are known in the art, see e.g., Mannino, et al., Biotechniques, 6:682, 1988. The composition of the liposome is usually a combination of phospholipids, usually in combination with steroids, especially cholesterol. Other phospholipids or other lipids may also be used. The physical characteristics of liposomes depend on pH, ionic strength, and the presence of divalent cations.

Examples of lipids useful in liposome production include phosphatidyl compounds, such as phosphatidylglycerol, phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingolipids, cerebrosides, and gangliosides. Illustrative phospholipids include egg phosphatidylcholine, dipalmitoylphosphatidylcholine, and distearoylphosphatidylcholine. The targeting of liposomes is also possible based on, for example, organ-specificity, cell-specificity, and organelle-specificity and is known in the art.

The disclosure provides formulations that may be varied to include acids and bases to adjust the pH; and buffering agents to keep the pH within a narrow range.

15. Kits

In certain embodiments, the disclosure also provides a pharmaceutical package or kit comprising one or more containers filled with at least one activin and/or GDF antagonist of the disclosure. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects (a) approval by the agency of manufacture, use or sale for human administration, (b) directions for use, or both.

EXEMPLIFICATION

The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain embodiments of the present invention, and are not intended to limit the invention.

Example 1 ActRIIa-Fc Fusion Proteins

A soluble ActRIIA fusion protein was constructed that has the extracellular domain of human ActRIIa fused to a human or mouse Fc domain with a minimal linker in between. The constructs are referred to as ActRIIA-hFc (SEQ ID NO: 177, Fc portion underlined) and ActRIIA-mFc, respectively.

The ActRIIA-hFc and ActRIIA-mFc proteins were expressed in CHO cell lines. Different leader sequences (e.g., the Honey bee melittin (HBML) leader (SEQ ID NO: 214), the Tissue plasminogen activator (TPA) leader (SEQ ID NO: 215), or the native leader (SEQ ID NO: 216)) may be used. An exemplary ActRIIA-hFc construct comprises the TPA leader and has the unprocessed amino acid sequence as set forth in SEQ ID NO: 178, encodable by a polynucleotide having the nucleic acid sequence of SEQ ID NO: 179.

Both ActRIIA-hFc and ActRIIA-mFc were remarkably amenable to recombinant expression. The exemplary ActRIIA-hFc protein was purified as a single, well-defined peak of protein. N-terminal sequencing revealed a single sequence of -ILGRSETQE (SEQ ID NO: 50). Purification could be achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange. The ActRIIA-hFc protein was purified to a purity of >98% as determined by size exclusion chromatography and >95% as determined by SDS PAGE. As shown in FIG. 7, the fusion protein purifies as a single, well-defined peak as visualized by sizing column (FIG. 7A) and Coomassie stained SDS-PAGE (FIG. 7B).

ActRIIA-hFc and ActRIIA-mFc showed a high affinity for ligands. GDF-11 or activin A were immobilized on a Biacore™ CM5 chip using standard amine-coupling procedure (FIG. 8). ActRIIA-hFc and ActRIIA-mFc proteins were loaded onto the system, and binding was measured. ActRIIA-hFc bound to activin with a dissociation constant (K_(D)) of 5×10⁻¹² and bound to GDF11 with a K_(D) of 9.96×10⁻⁹. ActRIIA-mFc behaved similarly.

The ActRIIA-hFc was very stable in pharmacokinetic studies. Rats were dosed with 1 mg/kg, 3 mg/kg, or 10 mg/kg of ActRIIA-hFc protein, and plasma levels of the protein were measured at 24, 48, 72, 144 and 168 hours. In a separate study, rats were dosed at 1 mg/kg, 10 mg/kg, or 30 mg/kg. In rats, ActRIIA-hFc had an 11-14 day serum half-life, and circulating levels of the drug were quite high after two weeks (11 μg/ml, 110 μg/ml, or 304 μg/ml for initial administrations of 1 mg/kg, 10 mg/kg, or 30 mg/kg, respectively.) In cynomolgus monkeys, the plasma half-life was substantially greater than 14 days, and circulating levels of the drug were 25 μg/ml, 304 μg/ml, or 1440 μg/ml for initial administrations of 1 mg/kg, 10 mg/kg, or 30 mg/kg, respectively.

Example 2 Alternative ActRIIA-Fc Proteins

A variety of ActRIIA variants that may be used to construct Fc-fusion proteins according to the methods described herein are described in the International Patent Application published as WO2006/012627 (see e.g., pp. 55-58), incorporated herein by reference in its entirety. An alternative construct may have a deletion of the C-terminal tail (the final 15 amino acids of the extracellular domain of ActRIIA). The amino acid sequence for such a construct is presented in SEQ ID NO: 180 (Fc portion underlined).

Example 3 Effects of an Exemplary ActRIIa-Fc Homodimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of the ActRIIa-Fc homodimers on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using similar methods to those mentioned in previous Examples and herein in the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with ActRIIa-Fc homodimer significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 17) and inflammatory (IL-1B and TNF-alpha, shown in FIG. 18) genes, inhibited the upregulation of TGF β1 and activin A (FIG. 19, top two panels), and reduced kidney injury (downregulation of NGAL, shown in FIG. 19, lower panel).

Example 4 Generation of ActRIIB-Fc Fusion Proteins

Applicants constructed a soluble ActRIIB fusion protein that has the extracellular domain of human ActRIIB fused to a human or mouse Fc domain with a minimal linker in between. The constructs are referred to as ActRIIB(20-134)-hFc (comprising the human ActRIIB extracellular domain (residues 20-134 of the native ActRIIB having the sequence of SEQ ID NO: 1) fused to a human Fc domain) and ActRIIB-mFc, respectively.

The ActRIIB(20-134)-hFc (SEQ ID NO: 181) and ActRIIB-mFc proteins were expressed in CHO cell lines. Three different leader sequences may be added to these sequences, such as: (i) the Honey bee melittin (HBML) leader (SEQ ID NO: 214), ii) the Tissue plasminogen activator (TPA) leader (SEQ ID NO: 215), and (iii) the Native leader (SEQ ID NO: 216). An exemplary ActRIIB(20-134)-hFc fusion protein with the TPA leader sequence has an unprocessed amino acid sequence of SEQ ID NO: 182, which is encodable by a polynucleotide having the nucleic acid sequence of SEQ ID NO: 183.

N-terminal sequencing of the CHO-cell-produced material revealed a major sequence of -GRGEAE (SEQ ID NO: 51). Notably, other constructs reported in the literature begin with an -SGR . . . sequence. Such reported constructs are also incorporated in the ActRIIB and its fusion proteins disclosed herein.

Purification could be achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange.

Applicants further generated an ActRIIB(25-131)-hFc fusion protein, which comprises the human ActRIIB extracellular domain with N-terminal and C-terminal truncations (residues 25-131 of the native ActRIIB having the sequence of SEQ ID NO: 1) fused N-terminally with a TPA leader sequence substituted for the native ActRIIB leader and C-terminally with a human Fc domain via a minimal linker (three glycine residues) (SEQ ID NO: 184). A polynucleotide encoding this fusion protein is shown in SEQ ID NO: 185. Applicants modified the codons and found a variant nucleic acid (SEQ ID NO: 186) encoding the ActRIIB(25-131)-hFc protein that provided substantial improvement in the expression levels of initial transformants. The processed ActRIIB(25-131)-hFc protein has an amino acid sequence of SEQ ID NO: 187 (N-terminus confirmed by N-terminal sequencing).

The expressed molecule was purified using a series of column chromatography steps, including for example, three or more of the following, in any order: Protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange.

Affinities of several ligands for ActRIIB(25-131)-hFc and its full-length counterpart ActRIIB(20-134)-hFc were evaluated in vitro with a Biacore™ instrument, and the results are summarized in the Table 3 below. Kd values were obtained by steady-state affinity fit due to very rapid association and dissociation of the complex, which prevented accurate determination of k_(on) and k_(off). ActRIIB(25-131)-hFc bound, for example, activin A, activin B, and GDF11 with high affinity.

TABLE 3 Ligand Selectivity of ActRIIB-hFc Variants Activin A Activin B GDF11 Fusion Construct (Kd, e⁻¹¹) (Kd, e⁻¹¹) (Kd, e⁻¹¹) ActRIIB(20-134)-hFc 1.6 1.2 3.6 ActRIIB(25-131)-hFc 1.8 1.2 3.1

Another exemplary ActRIIB-hFc fusion protein has the amino acid sequence of SEQ ID NO: 188, comprising an ActRIIB-derived portion (SEQ ID NO: 189, containing a L79D substitution of the corresponding ActRIIB extracellular domain sequence) fused to a human Fc domain. Either the ActRIIB-derived portion or the full-length of the ActRIIB-hFc fusion protein may be used as a monomer or as a non-Fc fusion protein as a monomer, dimer, or greater-order complex.

The ActRIIB(L79D, 20-134)-hFc fusion protein was expressed in CHO cell lines. Three different leader sequences may be used for the expression: (i) the Honey bee melittin (HBML) leader (SEQ ID NO: 214), (ii) the tissue plasminogen activator (TPA) leader (SEQ ID NO: 215), and (iii) the native leader (SEQ ID NO: 216). An exemplary ActRIIB(L79D, 20-134)-hFc fusion protein contains the TPA leader and has the unprocessed amino acid sequence of SEQ ID NO: 190. A polynucleotide encoding such exemplary fusion protein has the nucleic acid sequence of SEQ ID NO: 191.

Example 5 Effects of an Exemplary ActRIIB(20-134)-Fc Homodimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of the ActRIIB(20-134)-Fc homodimer on kidney disease were assessed in a mouse unilateral ureteral obstruction model, with similar methods mentioned in previous Examples and herein in the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with ActRIIB(20-134)-Fc homodimer significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 20) and inflammatory (IL-1B and TNF-alpha, shown in FIG. 21) genes, inhibited the upregulation of TGF β1 and activin A (FIG. 22, top two panels), and reduced kidney injury (downregulation of NGAL, shown in FIG. 22, lower panel).

Example 6 Generation of a Fusion Protein with Truncated ActRIIB Extracellular Domain

As illustrated in Example 4, an ActRIIB(L79D, 20-134)-hFc fusion protein (SEQ ID NO: 190) was generated by N-terminal fusion of TPA leader to the ActRIIB extracellular domain (residues 20-134 in SEQ ID NO: 1) containing a leucine-to-aspartate substitution (at residue 79 in SEQ ID NO: 1) and C-terminal fusion of human Fc domain with minimal linker (three glycine residues). Further, a similar fusion protein with a truncated ActRIIB extracellular domain, referred to as ActRIIB(L79D, 25-131)-hFc (SEQ ID NO: 192), was generated by N-terminal fusion of TPA leader to truncated extracellular domain (residues 25-131 in SEQ ID NO: 1) containing a leucine-to-aspartate substitution (at residue 79 in SEQ ID NO: 1) and C-terminal fusion of human Fc domain with minimal linker (three glycine residues). The sequence of the cell purified form of ActRIIB(L79D, 25-131)-hFc is presented in SEQ ID NO: 193. One nucleotide sequence encoding this fusion protein is shown in SEQ ID NO: 194, while an alternative polynucleotide sequence encoding exactly the same fusion protein is shown in SEQ ID NO: 195.

The affinity of these and other ActRIIB-hFc proteins for several ligands was evaluated in vitro with a Biacore™ instrument. Results are summarized in the Table 4 below. K_(d) values were obtained by steady-state affinity fit due to the very rapid association and dissociation of the complex, which prevented accurate determination of k_(on) and k_(off).

TABLE 4 Ligand Selectivity of ActRIIB-hFc Variants Activin A Activin B GDF11 Fusion Construct (K_(d), e⁻¹¹) (K_(d), e⁻¹¹) (K_(d), e⁻¹¹) ActRIIB(20-134)-hFc 1.6 1.2 3.6 ActRIIB(L79D, 20-134)-hFc 1350.0 78.8 12.3 ActRIIB(25-131)-hFc 1.8 1.2 3.1 ActRIIB(L79D, 25-131)-hFc 2290.0 62.1 7.4

The fusion protein with a truncated extracellular domain, ActRIIB(L79D, 25-131)-hFc, equaled or surpassed the ligand selectivity for Activin B and GDF11 displayed by the longer variant, ActRIIB(L79D, 20-134)-hFc, with pronounced loss of activin A binding, partial loss of activin B binding, and nearly full retention of GDF11 binding compared to ActRIIB-hFc counterparts lacking the L79D substitution. Note that different truncation variants without the L79D substitution (i.e., ActRIIB(25-131)-hFc vs. ActRIIB(20-134)-hFc) had similar binding selectivity toward the ligands displayed here. ActRIIB(L79D, 25-131)-hFc also retains strong to intermediate binding to the Smad2/3 signaling ligand GDF8 and the Smad1/5/8 ligands BMP6 and BMP10.

Example 7 Effects of an Exemplary ActRIIB(L79D, 25-131)-hFc Homodimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of the ActRIIB(L79D, 25-131)-hFc homodimer on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using similar methods to those mentioned in previous Examples and herein in the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the ActRIIB(L79D, 25-131)-hFc homodimer did not suppress the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 44) or inflammatory (IL-1B and TNF-alpha, shown in FIG. 45) genes. The treatment did not inhibit the upregulation of TGF β1 and activin A (FIG. 46) or reduce kidney injury (downregulation of NGAL, shown in FIG. 46), either.

Example 8 Generation of an ALK4:ActRIIB Heterodimer

Applicants constructed a soluble ALK4-Fc:ActRIIB-Fc heteromeric complex comprising the extracellular domains of human ActRIIB and human ALK4, which are each separately fused to an Fc domain with a linker positioned between the extracellular domain and the Fc domain. The individual constructs are referred to as ActRIIB-Fc fusion polypeptide and ALK4-Fc fusion polypeptide, respectively, and the sequences for each are provided below. In this and other Examples, it is noted that the ActRIIB portion of the fusion protein used for forming dimers may comprise any part of natural or mutated ActRIIB sequences. For example, the ActRIIB portion may comprise a full-length extracellular domain of nature ActRIIB (e.g., an ActRIIB(20-134) sequence), an extracellular domain with truncations (e.g., an ActRIIB(25-131) sequence), extensions, or mutations (e.g., an ActRIIB(L79D, 25-131) or an ActRIIB(L79D, 20-134) sequence), unless specified otherwise.

A methodology for promoting formation of ALK4-Fc:ActRIIB-Fc heteromeric complexes, as opposed to ActRIIB-Fc or ALK4-Fc homodimeric complexes, is to introduce alterations in the amino acid sequence of the Fc domains to guide the formation of asymmetric heteromeric complexes. Many different approaches to making asymmetric interaction pairs using Fc domains are described in this disclosure.

In addition to the structures shown in FIGS. 5 and 6, ALK4:ActRIIB heterodimers may be formed in other multimeric structures, such as those in FIGS. 9 and 11. Possible monomers for the multimeric complex include the various fusion proteins exemplified in FIG. 10.

In one approach, illustrated in the ActRIIB-Fc (SEQ ID NO: 199 or 201) and ALK4-Fc (SEQ ID NO: 202 or 204) polypeptide sequences, one Fc domain is altered to introduce cationic amino acids at the interaction face, while the other Fc domain is altered to introduce anionic amino acids at the interaction face. ActRIIB-Fc fusion polypeptide and ALK4-Fc fusion polypeptide each employ the tissue plasminogen activator (TPA) leader (SEQ ID NO: 215).

In SEQ ID NO: 199, the leader (signal) sequence and linker are underlined. To promote formation of ALK4-Fc:ActRIIB-Fc heterodimer rather than ActRIIB-Fc:ActRIIB-Fc or ALK4-Fc:ALK4-Fc homodimeric complexes, two amino acid substitutions (replacing acidic amino acids with lysine) can be introduced into the Fc domain of the ActRIIB fusion protein, as indicated by double underline in SEQ ID NO: 199. The corresponding processed protein (i.e., no leader sequence) has the amino acid sequence of SEQ ID NO: 201. The amino acid sequences of SEQ ID NO: 199 or 201 may optionally be provided with lysine (K) removed from the C-terminus. A polynucleotide encoding SEQ ID NO: 199 has a nucleic acid sequence of SEQ ID NO: 200.

The corresponding ALK4-Fc fusion polypeptide having the amino acid sequence of SEQ ID NO: 202, with the leader sequence and linker underlined). To guide heterodimer formation with the ActRIIB-Fc fusion polypeptide of SEQ ID NOs: 199 and 201 above, two amino acid substitutions (replacing lysines with aspartic acids) can be introduced into the Fc domain of the ALK4-Fc fusion polypeptide as indicated by double underline in SEQ ID NO: 202. The corresponding processed protein (i.e., without the leader sequence) has the amino acid sequence of SEQ ID NO: 204. The amino acid sequences of SEQ ID NOs: 202 and 204 may optionally be provided with lysine (K) added at the C-terminus. One polynucleotide encoding SEQ ID NO: 202 has a nucleic acid sequence of SEQ ID NO: 203.

The ActRIIB-Fc (SEQ ID NO: 199 or 201, or the corresponding sequences having the lysine (K) removed from the C terminus) and ALK4-Fc proteins (SEQ ID NO: 202 or 204, or the corresponding sequences having a lysine (K) added to the C terminus) may be co-expressed and purified from a CHO cell line, to give rise to a heteromeric complex comprising ALK4-Fc:ActRIIB-Fc.

In another approach to promote the formation of heteromultimer complexes using asymmetric Fc fusion proteins, the Fc domains are altered to introduce complementary hydrophobic interactions and an additional intermolecular disulfide bond as illustrated in the ActRIIB-Fc and ALK4-Fc polypeptide sequences of SEQ ID NOs: 205 or 206 and 207 or 208, respectively. The ActRIIB-Fc fusion polypeptide and ALK4-Fc fusion polypeptide each employ the tissue plasminogen activator (TPA) leader (SEQ ID NO: 215).

In an ActRIIB-Fc polypeptide sequence set forth in SEQ ID NO: 205, the leader (signal) sequence and linker are underlined. To promote formation of the ALK4-Fc:ActRIIB-Fc heterodimer rather than homodimeric complexes, two amino acid substitutions (replacing a serine with a cysteine and a threonine with a tryptophan) can be introduced into the Fc domain of the fusion protein as indicated by double underline above. The corresponding processed protein (i.e., without the leader sequence) has the amino acid sequence of SEQ ID NO: 206. The amino acid sequences of SEQ ID NOs: 205 and 206 may optionally be provided with lysine (K) removed from the C-terminus.

In an ALK4-Fc polypeptide sequence set forth in SEQ ID NO: 207, the leader sequence and the linker are underlined. To guide heterodimer formation with the ActRIIB-Fc fusion polypeptide of SEQ ID NOs: 205 or 206 above, four amino acid substitutions can be introduced into the Fc domain of the ALK4 fusion polypeptide as indicated by double underline in SEQ ID NO: 207. The corresponding processed protein (i.e., without the leader sequence) has the amino acid sequence of SEQ ID NO: 208. The amino acid sequences of SEQ ID NOs: 207 and 208 may optionally be provided with lysine (K) removed from the C-terminus.

ActRIIB-Fc (SEQ ID NO: 205 or 206, or the corresponding sequences having the lysine (K) removed from the C terminus) and ALK4-Fc proteins (SEQ ID NO: 207 or 208, or the corresponding sequences having the lysine (K) removed from the C terminus) may be co-expressed and purified from a CHO cell line, to give rise to a heteromeric complex comprising ALK4-Fc:ActRIIB-Fc.

Purification of various ALK4-Fc:ActRIIB-Fc complexes could be achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange.

Example 9 Ligand Binding Profile of ALK4-Fc:ActRIIB-Fc Heterodimer Compared to ActRIIB-Fc Homodimer and ALK4-Fc Homodimer

A Biacore™-based binding assay was used to compare ligand binding selectivity of an exemplary ALK4-Fc:ActRIIB-Fc heterodimeric complex as described above with the binding selectivity of ActRIIB-Fc and ALK4-Fc homodimer complexes. The ALK4-Fc:ActRIIB-Fc heterodimer, ActRIIB-Fc homodimer, and ALK4-Fc homodimer were independently captured onto the system using an anti-Fc antibody. Ligands were injected and allowed to flow over the captured receptor protein. Results are summarized in the Table 5 below, in which ligand off-rates (k_(d)) most indicative of effective ligand traps are denoted by gray shading.

TABLE 5 Ligand binding profile of ALK4-Fc:ActRIIB-Fc:heterodimer compared to ActRIIB-Fc homodimer and ALK4-Fc homodimer ActRIIB-Fc ALK4-Fc ALK4-Fc:ActRIIB-Fc homodimer homodimer heterodimer k_(a) k_(d) K_(D) k_(a) k_(d) K_(D) k_(a) k_(d) K_(D) Ligand (1/Ms) (1/s) (pM) (1/Ms) (1/s) (pM) (1/Ms) (1/s) (pM) Activin A 1.2 × 10⁷ 2.3 × 10⁻⁴ 19 5.8 × 10⁵ 1.2 × 10⁻² 20000  1.3 × 10⁷ 1.5 × 10⁻⁴ 12 Activin B 5.1 × 10⁶ 1.0 × 10⁻⁴ 20 No binding 7.1 × 10⁶ 4.0 × 10⁻⁵ 6 BMP6 3.2 × 10⁷ 6.8 × 10⁻³ 190 — 2.0 × 10⁶ 5.5 × 10⁻³ 2700 BMP9 1.4 × 10⁷ 1.1 × 10⁻³ 77 — Transient* 3400 BMP10 2.3 × 10⁷ 2.6 × 10⁻⁴ 11 — 5.6 × 10⁷ 4.1 × 10⁻³ 74 GDF3 1.4 × 10⁶ 2.2 × 10⁻³ 1500 — 3.4 × 10⁶ 1.7 × 10⁻² 4900 GDF8 8.3 × 10⁵ 2.3 × 10⁻⁴ 280 1.3 × 10⁵ 1.9 × 10⁻³ 15000† 3.9 × 10⁵ 2.1 × 10⁻⁴ 550 GDF11 5.0 × 10⁷ 1.1 × 10⁻⁴ 2 5.0 × 10⁶ 4.8 × 10⁻³  270† 3.8 × 10⁷ 1.1 × 10⁻⁴ 3 *Indeterminate due to transient nature of interaction †Very low signal — Not tested

These comparative binding data demonstrate that ALK4-Fc:ActRIIB-Fc heterodimer has an altered binding profile/selectivity relative to either ActRIIB-Fc or ALK4-Fc homodimers. ALK4-Fc:ActRIIB-Fc heterodimer displays enhanced binding to activin B compared with either homodimer, retains strong binding to activin A, GDF8, and GDF11 as observed with ActRIIB-Fc homodimer, and exhibits substantially reduced binding to BMP9, BMP10, and GDF3. In particular, BMP9 displays low or no observable affinity for ALK4-Fc:ActRIIB-Fc heterodimer, whereas this ligand binds strongly to ALK4-Fc:ActRIIB-Fc heterodimer. Like the ActRIIB-Fc homodimer, the heterodimer retains intermediate-level binding to BMP6. See FIG. 12.

In addition, an A-204 Reporter Gene Assay was used to evaluate the effects of ALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fc homodimer on signaling by activin A, activin B, GDF11, GDF8, BMP10, and BMP9. Cell line: Human Rhabdomyosarcoma (derived from muscle). Reporter vector: pGL3(CAGA)12 (as described in Dennler et al., 1998, EMBO 17: 3091-3100). The CAGA12 motif is present in TGF-beta responsive genes (PAI-1 gene), so this vector is of general use for factors signaling through Smad2 and 3. An exemplary A-204 Reporter Gene Assay is outlined below.

-   -   Day 1: Split A-204 cells into 48-well plate.     -   Day 2: A-204 cells transfected with 10 ug pGL3(CAGA)12 or         pGL3(CAGA)12(10 ug)+pRLCMV (1 ug) and Fugene.     -   Day 3: Add factors (diluted into medium+0.1% BSA). Inhibitors         need to be pre-incubated with Factors for about one hr before         adding to cells. About six hrs later, cells are rinsed with PBS         and then lysed.

Following the above steps, applicant performed a Luciferase assay.

Both the ALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fc homodimer were determined to be potent inhibitors of activin A, activin B, GDF11, and GDF8 in this assay. In particular, as can be seen in the comparative homodimer/heterodimer IC₅₀ data illustrated in FIG. 13, ALK4-Fc:ActRIIB-Fc heterodimer inhibits activin A, activin B, GDF8, and GDF11 signaling pathways similarly to the ActRIIB-Fc:ActRIIB-Fc homodimer. However, ALK4-Fc:ActRIIB-Fc heterodimer inhibition of BMP9 and BMP10 signaling pathways is significantly reduced compared to the ActRIIB-Fc:ActRIIB-Fc homodimer. This data is consistent with the above-discussed binding data in which it was observed that both the ALK4-Fc:ActRIIB-Fc heterodimer and ActRIIB-Fc:ActRIIB-Fc homodimer display strong binding to activin A, activin B, GDF8, and GDF11, but BMP10 and BMP9 have significantly reduced affinity for the ALK4-Fc:ActRIIB-Fc heterodimer compared to the ActRIIB-Fc:ActRIIB-Fc homodimer.

Together, these data therefore demonstrate that ALK4-Fc:ActRIIB-Fc heterodimer is a more selective antagonist of activin B, activin A, GDF8, and GDF11 compared to ActRIIB-Fc homodimer. Accordingly, an ALK4-Fc:ActRIIB-Fc heterodimer will be more useful than an ActRIIB-Fc homodimer in certain applications where such selective antagonism is advantageous. Examples include therapeutic applications where it is desirable to retain antagonism of one or more of activin A, activin B, activin AB, GDF8, and GDF11 but minimize antagonism of one or more of BMP9, BMP10, GDF3, and BMP6.

Example 10 Effects of an Exemplary ALK4:ActRIIB Heteromultimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of the ALK4-Fc:ActRIIB-Fc heterodimer described in Example 7 on kidney disease was assessed in a mouse unilateral ureteral obstruction model. See, e.g., Klahr and Morrissey (2002) Am J Physiol Renal Physiol 283: F861-F875.

Twenty-four C57BL/6 male mice 12 weeks of age underwent left unilateral ureteral ligation twice at the level of the lower pole of kidney. After 3 days, eight mice were euthanized and kidneys from individual animals were harvested to assess kidney injury. The remaining mice were randomized into two groups: i) eight mice were injected subcutaneously with the ALK4-Fc:ActRIIB-Fc heterodimer at a dose of 10 mg/kg at day 3, day 7, day 10, and day 14 after surgery and a ii) eight mice were injected subcutaneously with vehicle control, phosphate buffered saline (PBS), at day 3, day 7, day 10, and day 14 after surgery. Both groups were sacrificed at day 17 in accordance with the relevant Animal Care Guidelines. Half kidneys from individual animals were collected for histology analysis (H&E, and Masson's Trichrome stain), from both the UUO kidney and contralateral kidney, and 1/4 kidneys were used for RNA extraction (RNeasy Midi Kit, Qiagen, IL).

Gene expression analysis on UUO kidney samples was performed to assess levels of various genes. QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic genes (Col1a1, Fibronectin, PAI-1, CTGF, and a-SMA), inflammatory genes (TNF-alpha, and MCP1), cytokines (TGFβ1, TGFβ2, TGFβ3, and activin A), and kidney injury genes (NGAL). See FIG. 14. Treatment of mice with ALK4-Fc:ActRIIB-Fc heterodimer significantly suppressed the expression of fibrotic and inflammatory genes, inhibited the upregulation of TGFβ 1/2/3 and reduced kidney injury. Histology data confirmed that ALK4-Fc:ActRIIB-Fc heterodimer treatment significantly inhibited kidney fibrosis and reduced kidney injury in the UUO model.

Together, these data demonstrate that ALK4:ActRIIB heteromultimer treatment suppresses kidney fibrosis and inflammation and reduces kidney injury. Moreover, these data indicate that other ALK4:ActRIIB antagonists may be useful in the treatment or preventing of kidney disease including, for example, antagonists of ALK4 and/or ActRIIB-binding ligands, antagonists of ALK4 and/or ActRIIB receptors, antagonists of ALK4 and/or ActRIIB downstream signaling mediators (e.g., Smads), and antagonists of TGFβ superfamily co-receptors associated with ALK4 and/or ActRIIB

Example 11 Generation of an ActRIIB-Fc:ALK7-Fc Heterodimer

Applicants constructed a soluble ActRIIB-Fc:ALK7-Fc heteromeric complex comprising the extracellular domains of human ActRIIB and human ALK7, which are each fused to an Fc domain with a linker positioned between the extracellular domain and the Fc domain. The individual constructs are referred to as ActRIIB-Fc and ALK7-Fc, respectively.

A methodology for promoting formation of ActRIIB-Fc:ALK7-Fc heteromeric complexes, as opposed to the ActRIIB-Fc or ALK7-Fc homodimeric complexes, is to introduce alterations in the amino acid sequence of the Fc domains to guide the formation of asymmetric heteromeric complexes. Many different approaches to making asymmetric interaction pairs using Fc domains are described in this disclosure.

In one approach, illustrated in the ActRIIB-Fc (SEQ ID NO: 199) and ALK7-Fc polypeptide sequences disclosed below, respectively, one Fc domain is altered to introduce cationic amino acids at the interaction face, while the other Fc domain is altered to introduce anionic amino acids at the interaction face. The ActRIIB-Fc fusion polypeptide and ALK7-Fc fusion polypeptide each employ the tissue plasminogen activator (TPA) leader (SEQ ID NO: 215).

The leader (signal) sequence and linker in SEQ ID NO: 199 are underlined. To promote formation of the ActRIIB-Fc:ALK7-Fc heterodimer rather than either of the possible homodimeric complexes, two amino acid substitutions (replacing acidic amino acids with lysine) can be introduced into the Fc domain of the ActRIIB fusion protein as indicated by double underline above. The corresponding processed (i.e., no leader sequence) ActRIIB-Fc fusion polypeptide has the amino acid sequence of SEQ ID NO: 201. Both SEQ ID NOs: 199 and 201 may optionally be provided with lysine (K) removed from the C-terminus. A polynucleotide encoding SEQ ID NO: 199 has a nucleic acid sequence of SEQ ID NO: 200.

An exemplary guided form of ALK7-Fc fusion protein is given in SEQ ID NO: 209. In the sequence, the signal sequence and linker sequence are underlined. To promote formation of the ActRIIB-Fc:ALK7-Fc heterodimer rather than homodimeric complexes, two amino acid substitutions (replacing lysines with aspartic acids) can be introduced into the Fc domain of the fusion protein as indicated by double underline. The corresponding processed (i.e., no leader sequence) ALK7-Fc fusion polypeptide has the amino acid sequence of SEQ ID NO: 211. Both SEQ ID NOs: 209 and 211 may optionally be provided with a lysine added at the C-terminus. A polynucleotide encoding SEQ ID NO: 209 has a nucleic acid sequence of SEQ ID NO: 210.

The ActRIIB-Fc (SEQ ID NO: 199 or 201, or the corresponding sequences having the lysine (K) removed from the C-terminus) and ALK7-Fc (SEQ ID NO: 209 or 211, or the corresponding sequences having a lysine (K) added at the C-terminus) proteins may be co-expressed and purified from a CHO cell line to give rise to a heteromeric complex comprising ActRIIB-Fc:ALK7-Fc.

In another approach to promote the formation of heteromultimer complexes using asymmetric Fc fusion proteins, the Fc domains are altered to introduce complementary hydrophobic interactions and an additional intermolecular disulfide bond in the Fc domains of the ActRIIB-Fc and ALK7-Fc polypeptides. For example, in a mutated ActRIIB-Fc polypeptide (SEQ ID NO: 205), the leader sequence and linker are underlined. To promote formation of the ActRIIB-Fc:ALK7-Fc heterodimer rather than either of the possible homodimeric complexes, two amino acid substitutions (replacing a serine with a cysteine and a threonine with a tryptophan) can be introduced into the Fc domain of the fusion protein as indicated by double underline above. The corresponding processed (i.e., no leader sequence) ActRIIB-Fc fusion polypeptide has the amino acid sequence of SEQ ID NO: 206. Both SEQ ID NOs: 205 and 206 may optionally be provided with lysine removed from the C-terminus.

An exemplary mutated form (for guided dimerization) of ALK7-Fc fusion protein is given in SEQ ID NO: 212. In the sequence, the leader and linker are underlined. To guide heterodimer formation with the ActRIIB-Fc fusion polypeptide of SEQ ID NO: 205 or 206 above, four amino acid substitutions can be introduced into the Fc domain of the ALK7 fusion polypeptide as indicated by double underline. The corresponding processed (i.e., no leader sequence) ALK7-Fc fusion polypeptide has the amino acid sequence of SEQ ID NO: 213. Both SEQ ID NOs: 212 and 213 may optionally be provided with the lysine removed from the C-terminus.

The ActRIIB-Fc (SEQ ID NO: 205 or 206, or the corresponding sequences having the lysine (K) removed from the C-terminus) and ALK7-Fc (SEQ ID NO: 212 or 213, or the corresponding sequences having the lysine (K) removed from the C-terminus) proteins may be co-expressed and purified from a CHO cell line, to give rise to a heteromeric complex comprising ActRIIB-Fc:ALK7-Fc.

Purification of various ActRIIB-Fc:ALK7-Fc complexes could be achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography. The purification could be completed with viral filtration and buffer exchange.

Example 12 Ligand Binding Profile of ActRIIB-Fc:ALK7-Fc Heterodimer Compared to ActRIIB-Fc Homodimer and ALK7-Fc Homodimer

A Biacore™-based binding assay was used to compare ligand binding selectivity of an exemplary ActRIIB-Fc:ALK7-Fc heterodimeric complex with that of ActRIIB-Fc and ALK7-Fc homodimeric complexes. Exemplary dimers such as an ActRIIB-Fc:ALK7-Fc heterodimer, an ActRIIB-Fc homodimer, and an ALK7-Fc homodimer were independently captured onto the system using an anti-Fc antibody. Ligands were injected and allowed to flow over the captured receptor protein. Results are summarized in the Table 6 below, in which ligand off-rates (k_(d)) most indicative of effective ligand traps are denoted by gray shading.

TABLE 6 Ligand binding profile of ActRIIB-Fc:ALK7-Fc heterodimer compared to ActRIIB-Fc homodimer and ALK7-Fc homodimer ActRIIB-Fc ALK7-Fc ActRIIB-Fc:ALK7-Fc homodimer homodimer heterodimer k_(a) k_(d) K_(D) k_(a) k_(d) K_(D) ka k_(d) K_(D) Ligand (1/Ms) (1/s) (pM) (1/Ms) (1/s) (pM) (1/Ms) (1/s) (pM) activin A 1.3 × 10⁷ 1.4 × 10⁻⁴ 11 No binding 4.4 × 10⁷ 1.9 × 10⁻³ 43 activin B 1.5 × 10⁷ 1.6 × 10⁻⁴ 8 No binding 1.2 × 10⁷ 2.0 × 10⁻⁴ 17 activin C No binding No binding 3.5 × 10⁵ 2.4 × 10⁻³ 6900 activin AC 2.0 × 10⁷ 3.1 × 10⁻³ 160 No binding 2.6 × 10⁶ 5.7 × 10⁻⁴ 220 BMP5 2.6 × 10⁷ 7.5 × 10⁻² 2900 No binding 1.5 × 10⁵ 8.5 × 10⁻³ 57000 BMP6 2.4 × 10⁷ 3.9 × 10⁻³ 160 No binding 1.2 × 10⁶ 6.3 × 10⁻³ 5300 BMP9 1.2 × 10⁸ 1.2 × 10⁻³ 10 No binding Transient* >1400 BMP10 5.9 × 10⁶ 1.5 × 10⁻⁴ 25 No binding 1.5 × 10⁷ 2.8 × 10⁻³ 190 GDF3 1.4 × 10⁶ 2.2 × 10⁻³ 1500 No binding 2.3 × 10⁶ 1.0 × 10⁻² 4500 GDF8 3.5 × 10⁶ 2.4 × 10⁻⁴ 69 No binding 3.7 × 10⁶ 1.0 × 10⁻³ 270 GDF11 9.6 × 10⁷ 1.5 × 10⁻⁴ 2 No binding 9.5 × 10⁷ 7.5 × 10⁻⁴ 8 *Indeterminate due to transient nature of interaction — Not tested

These comparative binding data demonstrate that the ActRIIB-Fc:ALK7-Fc heterodimer has an altered binding profile/selectivity relative to either the ActRIIB-Fc homodimer or ALK7-Fc homodimer. Interestingly, four of the five ligands with the strongest binding to ActRIIB-Fc homodimer (activin A, BMP10, GDF8, and GDF11) exhibit reduced binding to the ActRIIB-Fc:ALK7-Fc heterodimer, the exception being activin B which retains tight binding to the heterodimer. Similarly, three of the four ligands with intermediate binding to ActRIIB-Fc homodimer (GDF3, BMP6, and particularly BMP9) exhibit reduced binding to the ActRIIB-Fc:ALK7-Fc heterodimer, whereas binding to activin AC is increased to become the second strongest ligand interaction with the heterodimer overall. Finally, activin C and BMP5 unexpectedly bind the ActRIIB-Fc:ALK7 heterodimer with intermediate strength despite no binding (activin C) or weak binding (BMP5) to ActRIIB-Fc homodimer. The net result is that the ActRIIB-Fc:ALK7-Fc heterodimer possesses a ligand-binding profile distinctly different from that of either ActRIIB-Fc homodimer or ALK7-Fc homodimer, which binds none of the foregoing ligands. See FIG. 15.

These results therefore demonstrate that the ActRIIB-Fc:ALK7-Fc heterodimer is a more selective antagonist of activin B and activin AC compared to ActRIIB-Fc homodimer. Moreover, ActRIIB-Fc:ALK7-Fc heterodimer exhibits the unusual property of robust binding to activin C. Accordingly, an ActRIIB-Fc:ALK7-Fc heterodimer will be more useful than an ActRIIB-Fc homodimer in certain applications where such selective antagonism is advantageous. Examples include therapeutic applications where it is desirable to retain antagonism of activin B or activin AC but decrease antagonism of one or more of activin A, GDF3, GDF8, GDF11, BMP9, or BMP10. Also included are therapeutic, diagnostic, or analytic applications in which it is desirable to antagonize activin C or, based on the similarity between activin C and activin E, activin E.

Example 13 Effects of an Exemplary ALK7:ActRIIB Heteromultimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of the ALK7-Fc:ActRIIB-Fc heterodimer described in Example 11 on kidney disease was assessed in a mouse unilateral ureteral obstruction model. See, e.g., Klahr and Morrissey (2002) Am J Physiol Renal Physiol 283: F861-F875.

Twenty-four C57BL/6 male mice 12 weeks of age underwent left unilateral ureteral ligation twice at the level of the lower pole of kidney. After 3 days, eight mice were euthanized and kidneys from individual animals were harvested to assess kidney injury. The remaining mice were randomized into two groups: i) eight mice were injected subcutaneously with the ALK7-Fc:ActRIIB-Fc heterodimer at a dose of 10 mg/kg at day 3, day 7, day 10, and day 14 after surgery and a ii) eight mice were injected subcutaneously with vehicle control, phosphate buffered saline (PBS), at day 3, day 7, day 10, and day 14 after surgery. Both groups were sacrificed at day 17 in accordance with the relevant Animal Care Guidelines. Half kidneys from individual animals were collected for histology analysis (H&E, and Masson's Trichrome stain), from both the UUO kidney and contralateral kidney, and 1/4 kidneys were used for RNA extraction (RNeasy Midi Kit, Qiagen, IL).

Gene expression analysis on UUO kidney samples was performed to assess levels of various genes. QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic genes (Col1a1, Col3a1, Fibronectin, PAI-1, CTGF, and a-SMA), inflammatory genes (TNF-alpha, and MCP1), cytokines (TGFβ1, TGFβ2, TGFβ3, and activin A), kidney injury genes (NGAL), Hypoxia-inducible factor 1-alpha (HIF1a), and activin A receptor (ActRIIA). See FIG. 16. Treatment of mice with ALK7-Fc:ActRIIB-Fc heterodimer significantly suppressed the expression of fibrotic and inflammatory genes, inhibited the upregulation of TGFβ 1/2/3, activin A, and ActRIIa, and reduced kidney injury. Histology data confirmed that ALK7-Fc:ActRIIB-Fc heterodimer treatment significantly inhibited kidney fibrosis and reduced kidney injury in the UUO model.

Together, these data demonstrate that ALK7:ActRIIB heteromultimer treatment suppresses kidney fibrosis and inflammation and reduces kidney injury. Moreover, these data indicate that other ALK7:ActRIIB antagonists may be useful in the treatment or preventing of kidney disease including, for example, antagonists of ALK7 and/or ActRIIB-binding ligands (e.g., ligand antibodies and other ligand traps such as follistatin, Cerberus and Lefty), antagonists of ALK7 and/or ActRIIB receptors, antagonists of ALK7 and/or ActRIIB downstream signaling mediators (e.g., Smads), and antagonists of TGFβ superfamily co-receptors (e.g., antagonists of Crypto or Cryptic).

Example 14 Effects of an Exemplary Anti-TGF Beta Pan Antibody on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-TGF-beta 1/2/3 pan antibody (i.e., binds to isoforms 1, 2, and 3 of TGF-beta) on kidney disease were assessed in a mouse unilateral ureteral obstruction model, with the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the pan antibody significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 23) and slightly decreased inflammatory (TNF-alpha, shown in FIG. 24) genes, and inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 25). However, different from the ActRIIA-Fc homodimer and the ActRIIB-Fc homodimer, the pan antibody did not reduce kidney injury (no downregulation of NGAL, shown in FIG. 25).

Example 15 Effects of an Exemplary Anti-Activin A Antibody on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-activin A antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-activin A antibody significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 26) and inflammatory (IL-1B and TNF-alpha, shown in FIG. 27) genes, inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 28), and reduced kidney injury (downregulation of NGAL, shown in FIG. 28).

Example 16 Effects of an Exemplary Anti-Activin A/B Antibody on Kidney Fibrosis, Inflammation, and Reduces Kidney Injury

The effects of an anti-activin A/B antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-activin A/B antibody significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 29) and inflammatory (IL-1B and TNF-alpha, shown in FIG. 30) genes, inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 31), and reduced kidney injury (downregulation of NGAL, shown in FIG. 31).

Example 17 Effects of an Exemplary Anti-Activin B Antibody Treatment on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-activin B antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-activin B antibody did not significantly suppress the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 32) or inflammatory (IL-1B and TNF-alpha, shown in FIG. 33) genes. The treatment did not significantly inhibit the upregulation of TGF β1/2/3 and activin A (FIG. 34) or reduce kidney injury (downregulation of NGAL, shown in FIG. 34), either.

Example 18 Effects of an Exemplary Anti-ActRIIA Antibody on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-ActRIIA antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-ActRIIA antibody significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 35) and inflammatory (TNF-alpha, shown in FIG. 36) genes, inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 37), and reduced kidney injury (downregulation of NGAL, shown in FIG. 37).

Example 19 Effects of an Exemplary Anti-ActRIIA/IIB Antibody on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-ActRIIA/IIB antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods to those mentioned in these Examples and herein in the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-ActRIIA/IIB antibody significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 38) and inflammatory (TNF-alpha, shown in FIG. 39) genes, inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 40), and reduced kidney injury (downregulation of NGAL, shown in FIG. 40).

Example 20 Effects of an Exemplary Anti-ActRIIB Antibody on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an anti-ActRIIB antibody on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

QRT-PCR was performed on a CFX Connect™ Real-time PCR detection system (Bio-Rad, CA) to evaluate the expression of various fibrotic and inflammatory genes and kidney injury genes (NGAL). Treatment of mice with the anti-ActRRIIB antibody did not suppress the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 41) or inflammatory (TNF-alpha, shown in FIG. 42) genes. The treatment did not inhibit the upregulation of TGF β1/2/3 and activin A (FIG. 43) or reduce kidney injury (downregulation of NGAL, shown in FIG. 43), either.

Example 21 Ligand Binding Profile of ALK4-Fc:ActRIIA-Fc Heterodimer Compared to ActRIIA-Fc Homodimer and ALK4-Fc Homodimer

Similarly, ActRIIA polypeptides (e.g., its extracellular domain) may be fused to, e.g., a human IgG Fc domain for further dimerization with itself (i.e., homodimers) or other polypeptides (i.e., heterodimers). In this and other Examples, it is noted that the ActRIIA portion of the fusion protein used for forming dimers may comprise any part of natural or mutated ActRIIA sequences disclosed herein or known in the art. For example, the ActRIIA portion may comprise a full-length extracellular domain of nature ActRIIA, an extracellular domain with truncations, extensions, or mutations, unless specified otherwise.

A Biacore™-based binding assay was used to compare ligand binding selectivity of an exemplary ALK4-Fc:ActRIIA-Fc heterodimeric complex with that of ActRIIA-Fc and ALK4-Fc homodimer complexes, using the same methods in these Examples and the instant description.

As shown in FIG. 49, these comparative binding data demonstrate that ALK4-Fc:ActRIIA-Fc heterodimer has an altered binding profile/selectivity relative to either ActRIIA-Fc or ALK4-Fc homodimers. ALK4-Fc:ActRIIA-Fc heterodimer displays enhanced binding to activin AC and activin A compared with either homodimer, retains strong binding to Activin AB as observed with ActRIIA-Fc homodimer, and exhibits substantially reduced binding to activin B, BMP10, and BMP7.

Example 22 Effects of an Exemplary ALK4-Fc:ActRIIA-Fc Heterodimer on Kidney Fibrosis, Inflammation, and Kidney Injury

The effects of an ALK4-Fc:ActRIIA-Fc heterodimer on kidney disease were assessed in a mouse unilateral ureteral obstruction model, using the same methods in these Examples and the instant description.

Treatment of mice with the ALK4-Fc:ActRIIA-Fc heterodimer significantly suppressed the expression of fibrotic (Col1a1, Col3a1, PAI-1, Fibronectin, CTGF, and a-SMA, shown in FIG. 50) and inflammatory (TNF-alpha, shown in FIG. 51) genes, inhibited the upregulation of TGF β1/2/3 and activin A (FIG. 52), and reduced kidney injury (downregulation of NGAL, shown in FIG. 52).

Example 23 Ligand Binding Profile of ALK4-Fc:BMPRII-Fc Heterodimer Compared to BMPRII-Fc Homodimer and ALK4-Fc Homodimer

A Biacore™-based binding assay was used to compare ligand binding selectivity of an exemplary ALK4-Fc:BMPRII-Fc heterodimeric complex with that of BMPRII-Fc and ALK4-Fc homodimer complexes, using the same methods in these Examples and the instant description.

As shown in FIG. 53, these comparative binding data demonstrate that ALK4-Fc:BMPRII-Fc heterodimer has an altered binding profile/selectivity relative to either BMPRII-Fc or ALK4-Fc homodimers. ALK4-Fc:BMPRII-Fc heterodimer displays enhanced binding to activin A, activin B and activin AB compared with either homodimer, retains intermediate binding to BMP10 as observed with BMPRII-Fc homodimer, and exhibits substantially reduced binding to BMP9 and BMP15.

Example 24 General Methods

Unless specified otherwise, materials and methods used in the above Examples are exemplified as below:

Generation of Human Fusion Proteins

Constructed fusion proteins are initially expressed by transient transfection in COS cells. In brief, COS cells (ATCC®) are transfected overnight with plasmids encoding target fusion proteins using FuGENE® 6 transfection reagent (Promega). The next day, cells are washed with phosphate-buffered saline, and serum-free medium is added. After incubation for 72 h, the COS-conditioned medium is harvested, filtered, and loaded on a MabSelect SuRe column (GE Healthcare, UK). Fusion proteins are eluted with 0.1 M glycine (pH 3.0), and the eluted fractions are immediately neutralized by addition 1 M Tris (pH 8.0) in a 1:10 ratio. Proteins are quantitated using a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Waltham, Mass.).

CHO cells are transfected by standard methods with plasmid encoding the target fusion proteins and containing a ubiquitous chromatin opening element (UCOE) to facilitate protein expression. See, e.g., Cytotechnology (2002) 38:43-46. Pools are selected in methotrexate (MTX) at concentrations of 10 nM, 20 nM, and 50 nM. The 50 nM MTX pool yields the highest expression level, so a dilution clone is obtained from this pool and adapted to serum-free suspension growth to generate conditioned media for purification.

Purification of Fusion Protein Derived from CHO Cells

Human fusion proteins expressed in CHO cells are purified as follows for subsequent characterization by surface plasmon resonance and reporter gene assays. Conditioned medium containing the target fusion protein is concentrated, filtered, and loaded on a MAb SelectSuRe column previously equilibrated with PBS. Resin is then washed with PBS, and the protein is eluted with 0.1M glycine pH 3.5. Fractions containing protein are neutralized with 5% (v/v) 1M Tris pH 8.0. The elution pool is loaded on a Q Sepharose FF 10 mL column (GE Healthcare) previously equilibrated with buffers A (50 mM Tris pH 8.0) and B (50 mM Tris, 1M NaCl pH 8.0). A wash is performed at 10% B (100 mM NaCl), followed by elution at 20% B (200 mM NaCl). Protein is further processed over HiLoad™ 26/60 Superdex (GE Healthcare) equilibrated in PBS containing 50 mM arginine (pH 7.22). Fractions are evaluated by analytical size-exclusion chromatography, and those containing over 90% monomer are pooled, concentrated, and characterized. Purity of samples is evaluated by analytical size-exclusion chromatography and SDS-PAGE with Coomassie staining.

Ligand Binding Profiles of Fusion Proteins

Surface plasmon resonance is used to investigate and characterize the binding between the fusion proteins and their binding partners. In an initial qualitative screen, recombinant fusion proteins are covalently immobilized on a BIACORE™ CM5 chip, and more than 30 ligands generated in-house or obtained from R&D Systems are injected individually over the captured fusion proteins to characterize their degree of binding at room temperature. Based on the results of this screen, Applicants subject selected ligands to quantitative characterization of binding to human fusion proteins at physiologic temperature. For one condition, fusion proteins are expressed in CHO cells, purified as described in Example 1, captured on a BIACORE™ chip with anti-Fc antibody, and tested by surface plasmon resonance with the following ligands at 37° C.

Inhibition of Ligand Binding to Fusion Proteins via Cell-Based Assays

Reporter gene assays are used to determine the ability of human fusion proteins to inhibit cell signaling (e.g., TGF-beta/Smad signaling). These assays are based on human cell lines transfected with a pGL3 BRE (comprising a TGF-beta/Smad response element) reporter plasmid as well as a Renilla reporter plasmid (pRLCMV) to control for transfection efficiency. TGF-beta response elements together with a promoter are present in the promoter of the pGL3 BRE reporter plasmid, so this vector is of general use for factors signaling through Smad proteins.

On the first day of the assay, cells are distributed in 48-well plates at 8.5×104 cells per well or 12.5×104 cells per well, respectively. On the second day, a solution containing 10 μg pGL3 BRE, 100 ng pRLCMV, 30 μl Fugene HD (Roche Applied Science, DE), and 970 μl OptiMEM™ (Invitrogen) is preincubated for 30 min, then added to assay buffer consisting of either Eagle's minimum essential medium, or McCoy's 5A medium, supplemented with 0.1% BSA. The mixture is applied to the plated cells (500 μl/well) for incubation overnight at 37° C.

On the third day, medium is removed, and cells are incubated overnight at 37° C. with a mixture of ligands and inhibitors prepared as described below. Fusion proteins are serially diluted in 200 μl volumes of assay buffer using a 48-well plate. An equal volume of assay buffer containing the test ligand is added to obtain a final ligand concentration equal to the EC50 determined previously. Test solutions are incubated at 37° C. for 30 minutes, then 250 μl of the mixture is added to all wells. Each concentration of test article is determined in duplicate. After incubation with test solutions overnight, cells are rinsed with phosphate-buffered saline, then lysed with passive lysis buffer (Promega E1941) and stored overnight at −70° C. On the fourth and final day, plates are warmed to room temperature with gentle shaking. Cell lysates are transferred in duplicate to a chemiluminescence plate (96-well) and analyzed in a luminometer with reagents from a Dual-Luciferase Reporter Assay system (Promega E1980) to determine normalized luciferase activity.

These assays are used to evaluate the ability of fusion proteins to inhibit cell signaling mediated by TGF-beta/Smad that Applicants identified by surface plasmon resonance as high-affinity binders. The fusion protein used in these assays is expressed in CHO cells and purified as described above.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.

While specific embodiments of the subject matter have been discussed, the above specification is illustrative and not restrictive. Many variations will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations. 

1. A method of treating or preventing kidney disease in a subject, comprising administering to the subject an activin and/or growth and differentiation factor (GDF) antagonist, wherein the antagonist inhibits one or more of activin, GDF8, GDF11, GDF3, GDF1, Nodal, activin receptor type IIA (ActRIIA), ActRIIB, activin receptor-like kinase 4 (ALK4), ALK5, ALK7, Cripto-1, Cryptic, Cryptic 1B, Smad2, and Smad3. 2-25. (canceled)
 26. The method of claim 1, wherein the antagonist is a multimeric polypeptide complex. 27-28. (canceled)
 29. The method of claim 26, wherein the antagonist comprises an antibody, or a biologically active fragment thereof, capable of binding to and inhibiting one or more of activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, activin BE, GDF8, GDF11, GDF3, GDF1, Nodal, Cripto-1, Cryptic, Cryptic 1B, ActRIIA, ActRIIB, ALK4, ALK5, ALK7, bone morphogenetic protein receptor type II (BMPRII), and MIS receptor type II (MISRII).
 30. The method of claim 26, wherein the antagonist comprises a ligand trap for one or more of activin A, activin B, activin C, activin AB, activin AC, activin BC, activin E, activin AE, activin BE, GDF8, GDF11, GDF3, GDF1, and Nodal.
 31. (canceled)
 32. The method of claim 26, wherein the antagonist comprises a polypeptide comprising an extracellular domain of one or more of ActRIIA, ActRIIB, ALK4, ALK5, ALK7, Cripto-1, Cryptic, and Cryptic 1B.
 33. The method of claim 26, wherein the antagonist is a dimer.
 34. (canceled)
 35. The method of claim 33 wherein the antagonist comprises an ActRIIA polypeptide and an ALK4 polypeptide, an ActRIIA polypeptide and an ALK5 polypeptide, an ActRIIA polypeptide and an ALK7 polypeptide, an ActRIIB polypeptide and an ALK4 polypeptide, an ActRIIB polypeptide and an ALK5 polypeptide, an ActRIIB polypeptide and an ALK7 polypeptide, an ActRIIA polypeptide and an ActRIIB polypeptide, an ActRIIA polypeptide and a BMPRII polypeptide, an ActRIIA polypeptide and a MISRII polypeptide, an ActRIIB polypeptide and a BMPRII polypeptide, an ActRIIB polypeptide and a MISRII polypeptide, an ALK4 polypeptide and an ALK5 polypeptide, an ALK4 polypeptide and an ALK7 polypeptide, an ALK5 polypeptide and an ALK7 polypeptide, an ALK4 polypeptide and a BMPRII polypeptide, an ALK4 polypeptide and a MISRII polypeptide, an ALK5 polypeptide and a BMPRII polypeptide, an ALK5 polypeptide and a MISRII polypeptide, an ALK7 polypeptide and a BMPRII polypeptide, an ALK7 polypeptide and a MISRII polypeptide, an ActRIIA polypeptide and a Cryptic polypeptide, an ActRIIA polypeptide and a Cripto-1 polypeptide, an ActRIIA polypeptide and a Cryptic 1B polypeptide, an ActRIIB polypeptide and a Cryptic polypeptide, an ActRIIB polypeptide and a Cripto-1 polypeptide, an ActRIIB polypeptide and a Cryptic 1B polypeptide, an ALK4 polypeptide and a Cryptic polypeptide, an ALK4 polypeptide and a Cripto-1 polypeptide, an ALK4 polypeptide and a Cryptic 1B polypeptide, an ALK5 polypeptide and a Cryptic polypeptide, an ALK5 polypeptide and a Cripto-1 polypeptide, an ALK5 polypeptide and a Cryptic 1B polypeptide, an ALK7 polypeptide and a Cryptic polypeptide, an ALK7 polypeptide and a Cripto-1 polypeptide, or an ALK7 polypeptide and a Cryptic 1B polypeptide.
 36. The method of claim 33, wherein the antagonist comprises an ActRIIA polypeptide and an ALK1 polypeptide, an ActRIIB polypeptide and an ALK4 polypeptide, an ALK1 polypeptide and an ALK4 polypeptide, an ALK1 polypeptide and an ALK5 polypeptide, an ALK1 polypeptide and an ALK7 polypeptide, a Cripto polypeptide and a Cryptic polypeptide, a Cryptic 1B polypeptide and a Cryptic polypeptide, a Cripto polypeptide and a Cryptic 1B polypeptide, an ALK1 polypeptide and a Cripto polypeptide, an ALK1 polypeptide and a Cryptic polypeptide, an ALK1 polypeptide and a Cryptic 1B polypeptide, a Cryptic polypeptide and a BMPRII polypeptide, a Cripto polypeptide and a BMPRII polypeptide, a Cryptic 1B polypeptide and a BMPRII polypeptide, a Cryptic polypeptide and a MISRII polypeptide, a Cripto polypeptide and a MISRII polypeptide, or a Cryptic 1B polypeptide and a MISRII polypeptide.
 37. The method of claim 33, wherein the antagonist comprises an ActRIIB polypeptide and an ALK4 polypeptide, an ActRIIB polypeptide and an ALK5 polypeptide, an ActRIIB polypeptide and an ALK7 polypeptide, an ActRIIA polypeptide and an ALK4 polypeptide, an ActRIIA polypeptide and an ALK5 polypeptide, or an ActRIIA polypeptide and an ALK7 polypeptide. 38-68. (canceled)
 69. The method of claim 33, wherein the antagonist is an ALK4 homodimer, an ALK5 homodimer, an ALK7 homodimer, an ActRIIA homodimer, an ActRIIB homodimer, a BMPRII homodimer, a MISRII homodimer, a Cripto-1 homodimer, a Cryptic-1B homodimer, or a Cryptic homodimer.
 70. The method of claim 1, wherein the antagonist is a fusion protein. 71-82. (canceled)
 83. The method of claim 1, wherein the antagonist is an ActRIIB-Fc-ALK7-Fc heterodimer comprising an ActRIIB-Fc polypeptide and an ALK7-Fc polypeptide, wherein the ActRIIB-Fc-ALK7-Fc heterodimer has increased binding activity to one or more of Activin AC, Activin C, and BMP5, and decreased binding activity to one or more of GDF11, GDF8, Activin A, BMP10, BMP6, GDF3, and BMP9 relative to an ActRIIB-Fc homodimer.
 84. The method of claim 1, wherein the antagonist is an ActRIIB-Fc-ALK3-Fc heterodimer comprising an ActRIIB-Fc polypeptide and an ALK3-Fc polypeptide, wherein the ActRIIB-Fc-ALK3-Fc heterodimer has increased binding activity to one or more of BMP2, BMP6, GDF7, GDF5, and BMP7, and decreased binding activity to one or more of BMP9, GDF3, Activin A, GDF11, GDF8, BMP10, and Activin B relative to an ActRIIB-Fc homodimer, and/or has increased binding activity to one or more of BMP4, BMP2, GDF6, BMP5, BMP6, GDF5, BMP7, and GDF7 relative to an ALK3-Fc homodimer.
 85. The method of claim 1, wherein the antagonist is an ActRIIB-Fc-ALK2-Fc heterodimer comprising an ActRIIB-Fc polypeptide and an ALK2-Fc polypeptide, wherein the ActRIIB-Fc-ALK2-Fc heterodimer has increased binding activity to one or more of BMP9 and BMP7, and decreased binding activity to one or more of GDF8, GDF11, GDF5, GDF3, GDF6, Activin A, and BMP10 relative to an ActRIIB-Fc homodimer.
 86. The method of claim 1, wherein the antagonist is an ActRIIA-Fc-ALK4-Fc heterodimer comprising an ActRIIA-Fc polypeptide and an ALK4-Fc polypeptide, wherein the ActRIIA-Fc-ALK4-Fc heterodimer has increased binding activity to one or more of Activin A, GDF11, Activin AC, and BMP6, and decreased binding activity to one or more of Activin B, BMP7, and BMP10 relative to an ActRIIA-Fc homodimer, and/or has increased binding activity to one or more of GDF8, GDF11, Activin A, and Active AB relative to an ALK4-Fc homodimer.
 87. The method of claim 1, wherein the antagonist is a BMPRII-Fc-ALK1-Fc heterodimer comprising a BMPRII-Fc polypeptide and an ALK1-Fc polypeptide, wherein the BMPRII-Fc-ALK1-Fc heterodimer has increased binding activity to one or more of BMP9 and BMP10, and decreased binding activity to BMP15 relative to an BMPRII-Fc homodimer, and/or has decreased binding activity to one or more of BMP9 and BMP10 relative to an ALK1-Fc homodimer.
 88. The method of claim 1, wherein the antagonist is a BMPRII-Fc-ALK3-Fc heterodimer comprising a BMPRII-Fc polypeptide and an ALK3-Fc polypeptide, wherein the BMPRII-Fc-ALK3-Fc heterodimer has increased binding activity to one or more of BMP2, BMP6, GDF6, and BMP10, and decreased binding activity to one or more of BMP9 and BMP15 relative to a BMPRII-Fc homodimer, and/or has increased binding activity to BMP6, and decreased binding activity to one or more of BMP4 and GDF5 relative to an ALK3-Fc homodimer.
 89. The method of claim 1, wherein the antagonist is a BMPRII-Fc-ALK4-Fc heterodimer comprising a BMPRII-Fc polypeptide and an ALK4-Fc polypeptide, wherein the BMPRII-Fc-ALK4-Fc heterodimer has increased binding activity to one or more of Activin A and Activin B, and decreased binding activity to one or more of BMP9 and BMP15 relative to a BMPRII-Fc homodimer, and/or has decreased binding activity to one or more of Activin A, Activin B, and Activin AB relative to an ALK4-Fc homodimer.
 90. (canceled)
 91. The method of claim 1, wherein the kidney disease comprises kidney fibrosis, kidney inflammation, and/or kidney injury.
 92. The method of claim 1, wherein the kidney disease comprises one or more of chronic kidney diseases (or failure), acute kidney diseases (or failure), primary kidney diseases, non-diabetic kidney diseases, glomerulonephritis, interstitial nephritis, diabetic kidney diseases, diabetic chronic kidney disease, diabetic nephropathy, glomerulosclerosis, rapid progressive glomerulonephritis, renal fibrosis, Alport syndrome, IDDM nephritis, mesangial proliferative glomerulonephritis, membranoproliferative glomerulonephritis, crescentic glomerulonephritis, renal interstitial fibrosis, focal segmental glomerulosclerosis, membranous nephropathy, minimal change disease, pauci-immune rapid progressive glomerulonephritis, IgA nephropathy, polycystic kidney disease, Dent's disease, nephrocytinosis, Heymann nephritis, polycystic kidney disease (e.g., autosomal dominant (adult) polycystic kidney disease and autosomal recessive (childhood) polycystic kidney disease), acute kidney injury, nephrotic syndrome, renal ischemia, podocyte diseases or disorders, proteinuria, glomerular diseases, membranous glomerulonephritis, focal segmental glomerulonephritis, pre-eclampsia, eclampsia, kidney lesions, collagen vascular diseases, benign orthostatic (postural) proteinuria, IgM nephropathy, membranous nephropathy, sarcoidosis, diabetes mellitus, kidney damage due to drugs, Fabry's disease, aminoaciduria, Fanconi syndrome, hypertensive nephrosclerosis, interstitial nephritis, acute interstitial nephritis, Sickle cell disease, hemoglobinuria, myoglobinuria, Wegener's Granulomatosis, Glycogen Storage Disease Type 1, chronic kidney disease, chronic renal failure, low Glomerular Filtration Rate (GFR), nephroangiosclerosis, lupus nephritis, ANCA-positive pauci-immune crescentic glomerulonephritis, chronic allograft nephropathy, nephrotoxicity, renal toxicity, kidney necrosis, kidney damage, glomerular and tubular injury, kidney dysfunction, nephritic syndrome, acute renal failure, chronic renal failure, proximal tubal dysfunction, acute kidney transplant rejection, chronic kidney transplant rejection, non-IgA mesangioproliferative glomerulonephritis, postinfectious glomerulonephritis, vasculitides with renal involvement of any kind, any hereditary renal disease, any interstitial nephritis, renal transplant failure, kidney cancer, kidney disease associated with other conditions (e.g., hypertension, diabetes, and autoimmune disease), Dent's disease, nephrocytinosis, Heymann nephritis, a primary kidney disease, a collapsing glomerulopathy, a dense deposit disease, a cryoglobulinemia-associated glomerulonephritis, an Henoch-Schonlein disease, a postinfectious glomerulonephritis, a bacterial endocarditis, a microscopic polyangitis, a Churg-Strauss syndrome, an anti-GBM-antibody mediated glomerulonephritis, amyloidosis, a monoclonal immunoglobulin deposition disease, a fibrillary glomerulonephritis, an immunotactoid glomerulopathy, ischemic tubular injury, a medication-induced tubulo-interstitial nephritis, a toxic tubulo-interstitial nephritis, an infectious tubulo-interstitial nephritis, a bacterial pyelonephritis, a viral infectious tubulo-interstitial nephritis which results from a polyomavirus infection or an HIV infection, a metabolic-induced tubulo-interstitial disease, a mixed connective disease, a cast nephropathy, a crystal nephropathy which may results from urate or oxalate or drug-induced crystal deposition, an acute cellular tubulo-interstitial allograft rejection, a tumoral infiltrative disease which results from a lymphoma or a post-transplant lymphoproliferative disease, an obstructive disease of the kidney, vascular disease, a thrombotic microangiopathy, a nephroangiosclerosis, an atheroembolic disease, a mixed connective tissue disease, a polyarteritis nodosa, a calcineurin-inhibitor induced-vascular disease, an acute cellular vascular allograft rejection, an acute humoral allograft rejection, early renal function decline (ERFD), end stage renal disease (ESRD), renal vein thrombosis, acute tubular necrosis, acute interstitial nephritis, established chronic kidney disease, renal artery stenosis, ischemic nephropathy, uremia, drug and toxin-induced chronic tubulointerstitial nephritis, reflux nephropathy, kidney stones, Goodpasture's syndrome, normocytic normochromic anemia, renal anemia, diabetic chronic kidney disease, IgG4-related disease, von Hippel-Lindau syndrome, tuberous sclerosis, nephronophthisis, medullary cystic kidney disease, renal cell carcinoma, adenocarcinoma, nephroblastoma, lymphoma, leukemia, hyposialylation disorder, chronic cyclosporine nephropathy, renal reperfusion injury, renal dysplasia, azotemia, bilateral arterial occlusion, acute uric acid nephropathy, hypovolemia, acute bilateral obstructive uropathy, hypercalcemic nephropathy, hemolytic uremic syndrome, acute urinary retention, malignant nephrosclerosis, postpartum glomerulosclerosis, scleroderma, non-Goodpasture's anti-GBM disease, microscopic polyarteritis nodosa, allergic granulomatosis, acute radiation nephritis, post-streptococcal glomerulonephritis, Waldenstrom's macroglobulinemia, analgesic nephropathy, arteriovenous fistula, arteriovenous graft, dialysis, ectopic kidney, medullary sponge kidney, renal osteodystrophy, solitary kidney, hydronephrosis, microalbuminuria, uremia, haematuria, hyperlipidemia, hypoalbuminaemia, lipiduria, acidosis, edma, tubulointerstitial renal fibrosis, hypertensive sclerosis, juxtaglomerular cell tumor, Fraser syndrome, Horseshoe kidney, renal tubular dysgenesis, hypokalemia, hypomagnesemia, hypercalcemia, hypophosphatemia, uromodulin-associated kidney disease, Nail-patella syndrome, lithium nephrotoxity, TNF-alpha nephrotoxicity, honeybee resin related renal failure, sugarcane harvesting acute renal failure, complete LCAT deficiency, Fraley syndrome, Page kidney, reflux nephropathy, Bardet-Biedl syndrome, collagenofibrotic glomerulopathy, Dent disease, Denys-Drash syndrome, congenital nephrotic syndrome, immunotactoid glomerulopathy, fibronextin glomerulopathy, Galloway Mowat syndrome, lipoprotein glomerulopathy, MesoAmerican nephropathy, beta-thalassemia renal disease, haemolytic uraemic syndrome, Henoch-Schonlein-Purpura disease, retroperitoneal fibrosis, polyarteritis nodose, cardiorenal syndrome, medullary kidney disease, renal artery stenosis, uromodulin kidney disease, and hyperkalemia.
 93. The method of claim 1, wherein the subject has unilateral ureter obstruction (UUO). 94-97. (canceled) 